I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 13 16:40:01 +14 2025 I: pbuilder-time-stamp: 1741833601 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2025.1-1.dsc] I: copying [./gromacs_2025.1.orig-regressiontests.tar.gz] I: copying [./gromacs_2025.1.orig.tar.gz] I: copying [./gromacs_2025.1-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gromacs_2025.1-1.dsc: unsupported subcommand dpkg-source: info: extracting gromacs in gromacs-2025.1 dpkg-source: info: unpacking gromacs_2025.1.orig.tar.gz dpkg-source: info: unpacking gromacs_2025.1.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2025.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 13 02:40 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=54947e4245df44e4980691a95347e00d LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3881455 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.vEj5qj1z/pbuilderrc_6oc9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vEj5qj1z/b2 --logfile b2/build.log gromacs_2025.1-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.4); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-mpi4py; however: Package python3-mpi4py is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on furo; however: Package furo is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-pygments; however: Package python3-pygments is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-copybutton; however: Package python3-sphinx-copybutton is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-inline-tabs; however: Package python3-sphinx-inline-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} furo{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libabsl20240722{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1t64{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libimath-3-1-29t64{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libjxl0.10{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnghttp3-9{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenexr-3-1-30{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpathplan4{a} libpciaccess0{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsvtav1enc2{a} libsynctex2{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-bs4{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-copybutton{a} python3-sphinx-inline-tabs{a} python3-sphinxcontrib.autoprogram{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-basic-ng{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation fonts-texgyre fonts-texgyre-math javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc publicsuffix python3-gdal python3-lxml python3-matplotlib python3-pil python3-pydot python3-pygraphviz python3-scipy python3-yaml ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 341 newly installed, 0 to remove and 0 not upgraded. Need to get 368 MB of archives. After unpacking 1676 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [136 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-18 [361 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3596 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bash-completion all 1:2.16.0-7 [319 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 44 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.9p2-1 [906 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 48 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0050 [42.7 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.6 [2336 B] Get: 51 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-1 [107 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 86 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250308 [115 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-1+b1 [23.3 MB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.7-1+b1 [12.0 MB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.7-1+b1 [6851 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2.1 [4519 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1 [274 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 108 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.1 [318 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.1 [387 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.1 [463 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-bs4 all 4.13.3-2 [166 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 132 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.1-1+b1 [119 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-2 [114 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 furo all 2024.08.06+dfsg-1 [62.8 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-18 [418 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-18 [9793 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-18 [14.5 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.42-3 [79.5 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-15.2 [14.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2 [190 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.04.0~dfsg-2+b1 [2351 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.04.0~dfsg-2+b1 [51.0 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.7-1 [11.5 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b3 [153 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.7-1 [15.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.7-1 [442 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libhwy1t64 arm64 1.2.0-2+b2 [499 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libimath-3-1-29t64 arm64 3.1.12-1+b3 [38.0 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libopenexr-3-1-30 arm64 3.1.13-1 [876 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libjxl0.10 arm64 0.10.4-2 [854 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libwmflite-0.2-7 arm64 0.2.13-1.1+b3 [72.0 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libgraphicsmagick-q16-3t64 arm64 1.4+really1.3.45+hg17689-1 [1071 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 graphicsmagick arm64 1.4+really1.3.45+hg17689-1 [1078 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-3 [39.2 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-3 [61.1 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.12.0-1 [1672 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libabsl20240722 arm64 20240722.0-1.5 [452 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-9+b1 [661 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1904.20250204-1 [137 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.2.0-1 [125 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.0-1 [1423 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-4 [415 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-3 [41.2 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-3 [629 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-3 [181 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-3 [198 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-3 [572 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-1 [57.1 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-1 [167 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 56.0-2 [58.5 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 56.0-2 [333 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-21+b1 [21.3 MB] Get: 232 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.124-1 [8180 B] Get: 234 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.124-1 [38.2 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.124-1 [21.8 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 6.2.4+ds-1 [58.3 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 6.1.2-3 [302 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-5+b1 [8826 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 241 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.1+b1 [10.6 MB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 244 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 56.0-2 [67.1 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.12.0-1 [142 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.5.4-4 [168 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.12.0-1 [238 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.12.0-1 [17.8 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 56.0-2 [28.5 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 56.0-2 [42.3 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-1 [101 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-1 [199 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 56.0-2 [642 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5+b1 [154 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libmuparser2v5 arm64 2.3.4-1+b1 [127 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libmuparser-dev arm64 2.3.4-1+b1 [33.5 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.6-5 [577 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.18.1+ds-2 [1017 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libopenmpi40 arm64 5.0.7-1 [2087 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 5.0.7-1 [97.2 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.6-5 [3931 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 5.0.7-1 [180 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 5.0.7-1 [1089 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5+b1 [48.2 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.2-1 [1970 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.2-1 [4678 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.2-2 [10.3 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5+b1 [60.6 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5+b1 [106 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.1 [59.4 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 lsb-release all 12.1-1 [5912 B] Get: 303 http://deb.debian.org/debian unstable/main arm64 mpi-default-bin arm64 1.18 [2576 B] Get: 304 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 305 http://deb.debian.org/debian unstable/main arm64 mscgen arm64 0.20-16 [45.1 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.19 [29.4 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.2-1 [505 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.2-2 [26.1 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 318 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 319 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 python3-mpi4py arm64 4.0.3-3 [634 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 323 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.5-1 [250 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-copybutton all 0.5.2-2 [17.9 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-inline-tabs all 2023.4.21-1 [35.9 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 rdfind arm64 1.6.0-1+b2 [39.1 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 symlinks arm64 1.4-5 [9312 B] Get: 332 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5+b1 [7357 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20250114-1 [22.8 MB] Get: 337 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20250114-1 [1282 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 341 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Fetched 368 MB in 5s (74.1 MB/s) Preconfiguring packages ... Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20765 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_arm64.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... 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Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libmunge2:arm64 (0.5.16-1) ... Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up libjbig2dec0:arm64 (0.20-1+b3) ... Setting up libteckit0:arm64 (2.5.12+ds1-1+b1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up bash-completion (1:2.16.0-7) ... Setting up libpathplan4:arm64 (2.42.4-3) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-16) ... Setting up libann0 (1.1.2+doc-9+b2) ... Setting up libdbus-1-3:arm64 (1.16.2-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... 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Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libgif7:arm64 (5.2.2-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up libnuma1:arm64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:arm64 (1.5.1-1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b2) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up librav1e0.7:arm64 (0.7.1-9+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-1) ... Setting up openmpi-common (5.0.7-1) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:arm64 (2.5.3-2) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.6-1) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libcdt5:arm64 (2.42.4-3) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libcgraph6:arm64 (2.42.4-3) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libpaper2:arm64 (2.2.5-0.3+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libmuparser2v5:arm64 (2.3.4-1+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up lsb-release (12.1-1) ... Setting up libfido2-1:arm64 (1.15.0-1+b1) ... Setting up libde265-0:arm64 (1.0.15-1+b3) ... Setting up openssl (3.4.1-1) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libdrm-common (2.4.124-1) ... Setting up libyuv0:arm64 (0.0.1904.20250204-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up libfmt10:arm64 (10.1.1+ds1-4) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2+b2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-18) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libmuparser-dev:arm64 (2.3.4-1+b1) ... Setting up libllvm19:arm64 (1:19.1.7-1+b1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libavif16:arm64 (1.2.0-1) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libclang1-19 (1:19.1.7-1+b1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:arm64 (1:3.5.17-1+b3) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-4) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.8-1) ... Setting up libpaper-utils (2.2.5-0.3+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:arm64 (3.7.0-1) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.5.4-4) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.84.0-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ... Setting up libllvm17t64:arm64 (1:17.0.6-21+b1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libopenexr-3-1-30:arm64 (3.1.13-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up ucf (3.0050) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:arm64 (2.42.4-3) ... Setting up libdrm2:arm64 (2.4.124-1) ... Setting up libnl-3-dev:arm64 (3.7.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-18) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up libhwloc-dev:arm64 (2.12.0-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-18) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libpython3-stdlib:arm64 (3.13.2-2) ... Setting up libclang-cpp19 (1:19.1.7-1+b1) ... Setting up libdrm-amdgpu1:arm64 (2.4.124-1) ... Setting up libjxl0.10:arm64 (0.10.4-2) ... Setting up libpython3.13:arm64 (3.13.2-1) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libibverbs1:arm64 (56.0-2) ... Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up ibverbs-providers:arm64 (56.0-2) ... Setting up python3.13 (3.13.2-1) ... Setting up openssh-client (1:9.9p2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libhwloc-plugins:arm64 (2.12.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b4) ... Setting up tex-common (6.19) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:arm64 (3.7.0-1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up doxygen (1.9.8+ds-2.1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libpython3.13-dev:arm64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-5) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libpmix2t64:arm64 (5.0.6-5) ... Setting up python3-numpy (1:2.2.3+ds-5) ... Setting up python3-urllib3 (2.3.0-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up librdmacm1t64:arm64 (56.0-2) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up python3-soupsieve (2.6-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpmix-dev:arm64 (5.0.6-5) ... Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up dh-python (6.20250308) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libxmu6:arm64 (2:1.1.3-3+b4) ... Setting up libpython3-dev:arm64 (3.13.2-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:arm64 (8.12.1-3) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.5-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.1) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libibverbs-dev:arm64 (56.0-2) ... Setting up pybind11-dev (2.13.6-2) ... Setting up python3-bs4 (4.13.3-2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-dev (3.13.2-2) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... Setting up cmake (3.31.6-1) ... Setting up python3-pybind11 (2.13.6-2) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up fontconfig-config (2.15.0-2.1) ... Setting up python3-networkx (3.2.1-5) ... Setting up libamdhip64-5 (5.7.1-5+b1) ... Setting up libfontconfig1:arm64 (2.15.0-2.1) ... Setting up libgs10:arm64 (10.04.0~dfsg-2+b1) ... Setting up fontconfig (2.15.0-2.1) ... Regenerating fonts cache... done. Setting up libucx0:arm64 (1.18.1+ds-2) ... Setting up libpango-1.0-0:arm64 (1.56.1-1) ... Setting up ghostscript (10.04.0~dfsg-2+b1) ... Setting up libcairo2:arm64 (1.18.2-2) ... Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ... Setting up texlive-base (2024.20250114-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ... Setting up libopenmpi40:arm64 (5.0.7-1) ... Setting up texlive-latex-base (2024.20250114-1) ... Setting up texlive-latex-recommended (2024.20250114-1) ... Setting up texlive-pictures (2024.20250114-1) ... Setting up texlive-fonts-recommended (2024.20250114-1) ... Setting up openmpi-bin (5.0.7-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.18) ... Setting up texlive-latex-extra (2024.20250114-1) ... Setting up python3-mpi4py (4.0.3-3) ... Setting up libopenmpi-dev:arm64 (5.0.7-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up libheif-plugin-libde265:arm64 (1.19.7-1) ... Setting up libheif1:arm64 (1.19.7-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-3) ... Setting up libheif-plugin-dav1d:arm64 (1.19.7-1) ... Setting up graphviz (2.42.4-3) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.45+hg17689-1) ... Setting up mscgen (0.20-16) ... Setting up graphicsmagick (1.4+really1.3.45+hg17689-1) ... Processing triggers for libc-bin (2.41-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinx-copybutton (0.5.2-2) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up sphinx-basic-ng (1.0.0~beta2-1) ... Setting up python3-sphinx-inline-tabs (2023.4.21-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Setting up furo (2024.08.06+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.19) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gromacs-2025.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gromacs_2025.1-1_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2025.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (61.4s) -- Generating done (4.3s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (96.6s) -- Generating done (4.0s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.7 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (114.0s) -- Generating done (4.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.7 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (81.8s) -- Generating done (2.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j12 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/errhandler.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_array.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 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-o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c 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/build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 2%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc3.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs 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/build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 2%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvaratoms.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 6%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 6%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 6%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_io.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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-I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/expandedensembleelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 10%] Built target options cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/logging.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 95%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/share/template /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/share/template 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api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/integrator.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/md.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs && 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/template.dir/link.d CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic 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"CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -j12 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT 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-DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 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-MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 4%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_meta.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/output.cpp [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_angles.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/reportgpuusage.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include 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-fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 12%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/mttk.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/nosehooverchains.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 12%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 14%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/enxio.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.10 -o ../../lib/libgromacs_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.10.0.0 ../../lib/libgromacs_d.so.10 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/resourceassignment.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/gmxcalculatorcpu.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/integrator.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/session.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ 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/build/reproducible-path/gromacs-2025.1/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples 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"CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -j12 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 78 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic 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VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 0%] Built target scanner [ 0%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake 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src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 2%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 2%] Built target energyanalysis [ 5%] Built target thread_mpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 8%] Built target colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: 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api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib 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/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && 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'/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target plumed_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f 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directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 64%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 65%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 65%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 65%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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"CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target domdec-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/position_restraints.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target fft-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target nbnxm-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 66%] Built target listed_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 67%] Built target awh-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF 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src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/simulationsignal.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 69%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 70%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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"CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 70%] Built target mdspan-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/exponentialmovingaverage.cpp cd 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/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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-o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 70%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 71%] Built target ewald-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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"CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target mdlib-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make 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CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target random-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target timing-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target pull-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/entropy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target taskassignment-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF 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/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 74%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/exclusionblocks.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 75%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 75%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make 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/build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/autocorr.cpp [ 75%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 75%] Built target gmxana-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 78%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 79%] Built target options-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 79%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target correlations-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" 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/build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' 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-I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 80%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 82%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 83%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/orires.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 84%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 84%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 85%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/topdirs.cpp [ 85%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 85%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/grompp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 85%] Built target selection-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/boxdeformation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY 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CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/termination.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 87%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make 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"CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ 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make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/gromacs-2025.1/build/basic' [ 88%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make 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"CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 89%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic 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/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o 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../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: 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"CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/bondtypes.cpp [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target nblib-integrator-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp [ 92%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/simstate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 92%] Built target gmxapi-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 93%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 93%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 [ 93%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 94%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/kernels.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 97%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 97%] Built target nblib-tests /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.1/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -8390889 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 30 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.127 0.068 186.1 1: (ns/day) (hour/ns) 1: Performance: 7.444 3.224 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (662 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1073889665 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 29 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.062 0.031 199.6 1: (ns/day) (hour/ns) 1: Performance: 16.327 1.470 1: [ OK ] GmxApiTest.RunnerBasicMD (357 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -200754 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.268 0.134 199.9 1: (ns/day) (hour/ns) 1: Performance: 26.458 0.907 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.257 0.129 199.9 1: (ns/day) (hour/ns) 1: Performance: 27.545 0.871 1: [ OK ] GmxApiTest.RunnerReinitialize (615 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1024475905 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 16 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.037 0.019 199.4 1: (ns/day) (hour/ns) 1: Performance: 27.332 0.878 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 18 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.5 1: (ns/day) (hour/ns) 1: Performance: 31.253 0.768 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (241 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1610063847 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 34 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.083 0.041 199.7 1: (ns/day) (hour/ns) 1: Performance: 20.348 1.179 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 30 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.037 0.019 199.3 1: (ns/day) (hour/ns) 1: Performance: 18.096 1.326 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (240 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 1449583289 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (151 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (2268 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (2298 ms total) 1: [ PASSED ] 9 tests. 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 2.63 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1212204867 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (207 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -9442824 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (146 ms) 2: [----------] 2 tests from GmxApiTest (354 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (365 ms total) 2: [ PASSED ] 2 tests. 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.38 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (18 ms) 3: [----------] 8 tests from NBlibTest (19 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (3 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (3 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (7 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (3 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (3 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (7 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (3 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (3 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (33 ms) 3: [----------] 1 test from LinearChainDataFixture (33 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (73 ms total) 3: [ PASSED ] 44 tests. 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.10 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.06 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/92 Test #6: NbLibUtilTests ............................ Passed 0.04 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (1 ms total) 7: [ PASSED ] 57 tests. 7/92 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (46 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (24 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (8 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 8: [----------] 4 tests from TprReaderTest (94 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (101 ms total) 8: [ PASSED ] 4 tests. 8/92 Test #8: NbLibTprTests ............................. Passed 0.14 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (3 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (3 ms total) 9: [ PASSED ] 20 tests. 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.04 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (2 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (4 ms total) 11: [ PASSED ] 75 tests. 11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.03 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (26 ms) 12: [----------] 1 test from MpiSelfTest (26 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (26 ms total) 12: [ PASSED ] 1 test. 12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.04 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (0 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (16 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (16 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (0 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (0 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (21 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/92 Test #13: UtilityUnitTests .......................... Passed 0.05 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (22 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (23 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (46 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (46 ms total) 14: [ PASSED ] 2 tests. 14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.07 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (5 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (6 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (7 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (6 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (3 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (93 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (93 ms total) 15: [ PASSED ] 78 tests. 15/92 Test #15: GmxlibTests ............................... Passed 0.13 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (3 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (3 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (3 ms) 16: [----------] 6 tests from CalcvirTest (11 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (4 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (3 ms) 16: [----------] 2 tests from PrEbinTest (8 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (11 ms) 16: [----------] 1 test from UpdateGroupsCog (11 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (3 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (16 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (31 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (73 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (19 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (23 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (8 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (11 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (119 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (3 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (4 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (7 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (3 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (4 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (3 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (4 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (3 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (3 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (3 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (34 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (8 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (8 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (7 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (15 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (30 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (100 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (6 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (8 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (315 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (164 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (124 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (59 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (7 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (7 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (60 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (55 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (11 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (6 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (7 ms) 16: [----------] 13 tests from WithParameters/SettleTest (28 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (1172 ms total) 16: [ PASSED ] 1032 tests. 16/92 Test #16: MdlibUnitTest ............................. Passed 1.29 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (4 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (4 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (8 ms) 17: [----------] 1 test from BiasTest (8 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (98 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (275 ms) 17: [----------] 2 tests from BiasSharingTest (374 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (13 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (15 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (4 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (10 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (16 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (11 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (10 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (30 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (23 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (25 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (478 ms total) 17: [ PASSED ] 27 tests. 17/92 Test #17: AwhTest ................................... Passed 0.50 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (10 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (7 ms) 18: [----------] 2 tests from DensityFittingTest (18 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (18 ms total) 18: [ PASSED ] 18 tests. 18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.03 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -469901485 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (10 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to 1316977805 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to 2067260793 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to 1475196922 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (42 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -372248593 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (14 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 19: Setting the LD random seed to -2013538827 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (18 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (90 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (6 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (3 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (11 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (3 ms) 19: [----------] 1 test from QMMMForceProviderTest (3 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (106 ms total) 19: [ PASSED ] 21 tests. 19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.13 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (4 ms) 20: [----------] 1 test from ColvarsTest (4 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (4 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (3 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -1094222149 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (53 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (61 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -1343236107 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -134350885 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -218628106 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (6 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -289155329 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (33 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (46 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (3 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -1375754370 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -646975665 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to -4728833 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (41 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 20: Setting the LD random seed to 1071510366 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (79 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (131 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (244 ms total) 20: [ PASSED ] 16 tests. 20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.27 sec test 21 Start 21: PlumedAppliedForcesUnitTests 21: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests 21: Test timeout computed to be: 30 21: [==========] Running 8 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 8 tests from PlumedOptionsTest 21: [ RUN ] PlumedOptionsTest.defaultConstructor 21: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 21: [ RUN ] PlumedOptionsTest.setTimeStep 21: [ OK ] PlumedOptionsTest.setTimeStep (7 ms) 21: [ RUN ] PlumedOptionsTest.setStartingBehavior 21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFile 21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 21: [ RUN ] PlumedOptionsTest.setTopology 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: 21: NOTE 2 [file angles1.top, line 72]: 21: In moleculetype 'butane' 4 atoms are not bound by a potential or 21: constraint to any other atom in the same moleculetype. Although 21: technically this might not cause issues in a simulation, this often means 21: that the user forgot to add a bond/potential/constraint or put multiple 21: molecules in the same moleculetype definition by mistake. Run with -v to 21: get information for each atom. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: NVE simulation: will use the initial temperature of 238.919 K for 21: determining the Verlet buffer size 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 17493.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: NVE simulation: will use the initial temperature of 67.983 K for 21: determining the Verlet buffer size 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 18.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: NVE simulation: will use the initial temperature of 135.187 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -12997 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -4850050 21: 21: Generated 3 of the 3 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'butane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -151063586 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Argon' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon5832.gro' 21: Analysing residue names: 21: There are: 5832 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -1781738561 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonA' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonB' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonC' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonD' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -169904423 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Dipole' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 21: Analysing residue names: 21: There are: 2 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -1262531586 21: 21: Generated 331705 of the 331705 non-bonded parameter combinations 21: 21: Generated 331705 of the 331705 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Excluding 3 bonded neighbours molecule type 'methane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 21: Analysing residue names: 21: There are: 1 Water residues 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] PlumedOptionsTest.setTopology (198 ms) 21: [----------] 8 tests from PlumedOptionsTest (206 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 8 tests from 1 test suite ran. (206 ms total) 21: [ PASSED ] 8 tests. 21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 0.23 sec test 22 Start 22: PlumedMDTests 22: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PlumedMDTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/plumed/tests 22: Test timeout computed to be: 600 22: [==========] Running 2 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from SimplePlumedMD/PlumedRun 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 22: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test suite ran. (8 ms total) 22: [ PASSED ] 0 tests. 22: [ SKIPPED ] 2 tests, listed below: 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22/92 Test #22: PlumedMDTests ............................. Passed 0.02 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (4 ms) 23: [----------] 1 test from NNPotTest (4 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (1 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to 1610087039 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to -269025311 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to 1052502895 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (8 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to -181121 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (8 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (22 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (28 ms total) 23: [ PASSED ] 12 tests. 23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.05 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (0 ms total) 24: [ PASSED ] 3 tests. 24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.02 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (4 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (7 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (4 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (3 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (49 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (4 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (8 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (4 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (8 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (3 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (8 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (7 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (160 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (7 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (7 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (3 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (7 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (7 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (3 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (39 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (7 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (3 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (32 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (7 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (3 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (3 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (16 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (3 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (3 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (6 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (3 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (12 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (3 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (3 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (3 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (11 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (325 ms total) 25: [ PASSED ] 132 tests. 25/92 Test #25: ListedForcesTest .......................... Passed 0.35 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 383 tests from 4 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (6 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (6 ms total) 26: 26: [----------] 2 tests from SimdEnergyAccumulatorTest 26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 26: 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (16 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (16 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (16 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (16 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (16 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (9 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (18 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (10 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (7 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (14 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (11 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (20 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (8 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (12 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (652 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 383 tests from 4 test suites ran. (659 ms total) 26: [ PASSED ] 185 tests. 26: [ SKIPPED ] 198 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/92 Test #26: NbnxmTests ................................ Passed 0.69 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/92 Test #27: NbnxmGpuTests ............................. Passed 0.03 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (30 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (31 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (10 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (7 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (18 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (51 ms total) 28: [ PASSED ] 60 tests. 28/92 Test #28: CommandLineUnitTests ...................... Passed 0.07 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/92 Test #29: DomDecTests ............................... Passed 0.02 sec test 30 Start 30: DomDecMpiTests 30: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (40 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (22 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (28 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (19 ms) 30: [----------] 4 tests from HaloExchangeTest (111 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (111 ms total) 30: [ PASSED ] 4 tests. 30/92 Test #30: DomDecMpiTests ............................ Passed 0.15 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (11 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (5 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (6 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (4 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (125 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from Pme_SolveTest (8 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (4 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (7 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [----------] 72 tests from Pme_GatherTest (10 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (23 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (185 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/92 Test #31: EwaldUnitTests ............................ Passed 0.24 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (2 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (4 ms) 32: [----------] 2 tests from ManyFFTTest (7 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 32: [----------] 1 test from FFTTest (1 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (8 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (19 ms total) 32: [ PASSED ] 15 tests. 32/92 Test #32: FFTUnitTests .............................. Passed 0.05 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (0 ms total) 33: [ PASSED ] 67 tests. 33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.04 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (0 ms) 34: [----------] 1 test from CpuInfoTest (0 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (15 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (15 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (10 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (14 ms) 34: [----------] 4 tests from HardwareTopologyTest (56 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (16 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (7 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (8 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (3 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (37 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (15 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (8 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (7 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (11 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (7 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (51 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (3 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (16 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (27 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (27 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (59 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (60 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (75 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (76 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (326 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/92 Test #34: HardwareUnitTests ......................... Passed 0.34 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (0 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (4 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (25 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (21 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (52 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (19 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 35: [----------] 2 tests from NelderMead (19 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (75 ms total) 35: [ PASSED ] 328 tests. 35/92 Test #35: MathUnitTests ............................. Passed 0.10 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (5 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 36: [----------] 17 tests from ThreadAffinityTest (7 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (7 ms total) 36: [ PASSED ] 21 tests. 36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.03 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (89 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (123 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (91 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (36 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (56 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (131 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (529 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (79 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (55 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (88 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (127 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (68 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (88 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (59 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (568 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (1097 ms total) 37: [ PASSED ] 13 tests. 37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 1.13 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (0 ms total) 38: [ PASSED ] 32 tests. 38/92 Test #38: MDSpanTests ............................... Passed 0.02 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 39: [----------] 2 tests from CheckpointDataTest (3 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (6 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (6 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (10 ms total) 39: [ PASSED ] 97 tests. 39/92 Test #39: MdtypesUnitTest ........................... Passed 0.03 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (3 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 40: [----------] 3 tests from HelpManagerTest (0 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (3 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (3 ms) 40: [----------] 11 tests from HelpWriterContextTest (10 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (15 ms total) 40: [ PASSED ] 22 tests. 40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.03 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (0 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (1 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (0 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (3 ms total) 41: [ PASSED ] 112 tests. 41/92 Test #41: OptionsUnitTests .......................... Passed 0.02 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 37 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (0 ms total) 42: 42: [----------] 5 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 42: [----------] 5 tests from PbcTest (0 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 37 tests from 5 test suites ran. (3 ms total) 42: [ PASSED ] 37 tests. 42/92 Test #42: PbcutilUnitTest ........................... Passed 0.02 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (0 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (0 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (0 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (1 ms total) 43: [ PASSED ] 44 tests. 43/92 Test #43: RandomUnitTests ........................... Passed 0.02 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (0 ms total) 44: [ PASSED ] 1 test. 44/92 Test #44: RestraintTests ............................ Passed 0.02 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 20 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (13 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (0 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (5 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (17 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 45: [ RUN ] SplineTableTest/0.Simd 45: [ OK ] SplineTableTest/0.Simd (10 ms) 45: [ RUN ] SplineTableTest/0.SimdTwoFunctions 45: [ OK ] SplineTableTest/0.SimdTwoFunctions (8 ms) 45: [----------] 10 tests from SplineTableTest/0 (66 ms total) 45: 45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (0 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (0 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (8 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 45: [ RUN ] SplineTableTest/1.Simd 45: [ OK ] SplineTableTest/1.Simd (0 ms) 45: [ RUN ] SplineTableTest/1.SimdTwoFunctions 45: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 45: [----------] 10 tests from SplineTableTest/1 (14 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 20 tests from 2 test suites ran. (81 ms total) 45: [ PASSED ] 20 tests. 45/92 Test #45: TableUnitTests ............................ Passed 0.11 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (0 ms total) 46: [ PASSED ] 3 tests. 46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.02 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (5 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (5 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (5 ms total) 47: [ PASSED ] 6 tests. 47/92 Test #47: GmxTimingTests ............................ Passed 0.03 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (6 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (1 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (5 ms) 48: [----------] 3 tests from IndexTest (14 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (0 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (0 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (5 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (20 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/92 Test #48: TopologyTest .............................. Passed 0.05 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (0 ms total) 49: [ PASSED ] 10 tests. 49/92 Test #49: PullTest .................................. Passed 0.02 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 288 tests from 22 test suites. 50: [----------] Global test environment set-up. 50: [----------] 9 tests from SimdBootstrapTest 50: [ RUN ] SimdBootstrapTest.loadStore 50: [ OK ] SimdBootstrapTest.loadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.loadU 50: [ OK ] SimdBootstrapTest.loadU (0 ms) 50: [ RUN ] SimdBootstrapTest.storeU 50: [ OK ] SimdBootstrapTest.storeU (0 ms) 50: [ RUN ] SimdBootstrapTest.loadStoreI 50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 50: [ RUN ] SimdBootstrapTest.loadUI 50: [ OK ] SimdBootstrapTest.loadUI (0 ms) 50: [ RUN ] SimdBootstrapTest.storeUI 50: [ OK ] SimdBootstrapTest.storeUI (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadStore 50: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadU 50: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4StoreU 50: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 50: [----------] 9 tests from SimdBootstrapTest (0 ms total) 50: 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (0 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (0 ms total) 50: 50: [----------] 1 test from SimdTest 50: [ RUN ] SimdTest.GmxAligned 50: [ OK ] SimdTest.GmxAligned (0 ms) 50: [----------] 1 test from SimdTest (0 ms total) 50: 50: [----------] 42 tests from SimdFloatingpointTest 50: [ RUN ] SimdFloatingpointTest.setZero 50: [ OK ] SimdFloatingpointTest.setZero (0 ms) 50: [ RUN ] SimdFloatingpointTest.set 50: [ OK ] SimdFloatingpointTest.set (0 ms) 50: [ RUN ] SimdFloatingpointTest.add 50: [ OK ] SimdFloatingpointTest.add (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskAdd 50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 50: [ RUN ] SimdFloatingpointTest.sub 50: [ OK ] SimdFloatingpointTest.sub (0 ms) 50: [ RUN ] SimdFloatingpointTest.mul 50: [ OK ] SimdFloatingpointTest.mul (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzMul 50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 50: [ RUN ] SimdFloatingpointTest.fma 50: [ OK ] SimdFloatingpointTest.fma (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzFma 50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fms 50: [ OK ] SimdFloatingpointTest.fms (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnma 50: [ OK ] SimdFloatingpointTest.fnma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnms 50: [ OK ] SimdFloatingpointTest.fnms (0 ms) 50: [ RUN ] SimdFloatingpointTest.abs 50: [ OK ] SimdFloatingpointTest.abs (0 ms) 50: [ RUN ] SimdFloatingpointTest.neg 50: [ OK ] SimdFloatingpointTest.neg (0 ms) 50: [ RUN ] SimdFloatingpointTest.and 50: [ OK ] SimdFloatingpointTest.and (0 ms) 50: [ RUN ] SimdFloatingpointTest.or 50: [ OK ] SimdFloatingpointTest.or (0 ms) 50: [ RUN ] SimdFloatingpointTest.xor 50: [ OK ] SimdFloatingpointTest.xor (0 ms) 50: [ RUN ] SimdFloatingpointTest.andNot 50: [ OK ] SimdFloatingpointTest.andNot (0 ms) 50: [ RUN ] SimdFloatingpointTest.max 50: [ OK ] SimdFloatingpointTest.max (0 ms) 50: [ RUN ] SimdFloatingpointTest.min 50: [ OK ] SimdFloatingpointTest.min (0 ms) 50: [ RUN ] SimdFloatingpointTest.round 50: [ OK ] SimdFloatingpointTest.round (0 ms) 50: [ RUN ] SimdFloatingpointTest.roundMode 50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 50: [ RUN ] SimdFloatingpointTest.trunc 50: [ OK ] SimdFloatingpointTest.trunc (0 ms) 50: [ RUN ] SimdFloatingpointTest.frexp 50: [ OK ] SimdFloatingpointTest.frexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.ldexp 50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.rsqrt 50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRsqrt 50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.rcp 50: [ OK ] SimdFloatingpointTest.rcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRcp 50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.selectByNotMask 50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpNe 50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLe 50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLt 50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 50: [ RUN ] SimdFloatingpointTest.testBits 50: [ OK ] SimdFloatingpointTest.testBits (0 ms) 50: [ RUN ] SimdFloatingpointTest.andB 50: [ OK ] SimdFloatingpointTest.andB (0 ms) 50: [ RUN ] SimdFloatingpointTest.orB 50: [ OK ] SimdFloatingpointTest.orB (0 ms) 50: [ RUN ] SimdFloatingpointTest.anyTrueB 50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 50: [ RUN ] SimdFloatingpointTest.blend 50: [ OK ] SimdFloatingpointTest.blend (0 ms) 50: [ RUN ] SimdFloatingpointTest.reduce 50: [ OK ] SimdFloatingpointTest.reduce (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 50: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 50: 50: [----------] 16 tests from SimdFloatingpointUtilTest 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 50: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 50: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 50: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 50: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 50: 50: [----------] 23 tests from SimdIntegerTest 50: [ RUN ] SimdIntegerTest.setZero 50: [ OK ] SimdIntegerTest.setZero (0 ms) 50: [ RUN ] SimdIntegerTest.set 50: [ OK ] SimdIntegerTest.set (0 ms) 50: [ RUN ] SimdIntegerTest.add 50: [ OK ] SimdIntegerTest.add (0 ms) 50: [ RUN ] SimdIntegerTest.sub 50: [ OK ] SimdIntegerTest.sub (0 ms) 50: [ RUN ] SimdIntegerTest.mul 50: [ OK ] SimdIntegerTest.mul (0 ms) 50: [ RUN ] SimdIntegerTest.and 50: [ OK ] SimdIntegerTest.and (0 ms) 50: [ RUN ] SimdIntegerTest.andNot 50: [ OK ] SimdIntegerTest.andNot (0 ms) 50: [ RUN ] SimdIntegerTest.or 50: [ OK ] SimdIntegerTest.or (0 ms) 50: [ RUN ] SimdIntegerTest.xor 50: [ OK ] SimdIntegerTest.xor (0 ms) 50: [ RUN ] SimdIntegerTest.extract 50: [ OK ] SimdIntegerTest.extract (0 ms) 50: [ RUN ] SimdIntegerTest.cvtR2I 50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvttR2I 50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvtI2R 50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpLt 50: [ OK ] SimdIntegerTest.cmpLt (0 ms) 50: [ RUN ] SimdIntegerTest.testBits 50: [ OK ] SimdIntegerTest.testBits (0 ms) 50: [ RUN ] SimdIntegerTest.andB 50: [ OK ] SimdIntegerTest.andB (0 ms) 50: [ RUN ] SimdIntegerTest.orB 50: [ OK ] SimdIntegerTest.orB (0 ms) 50: [ RUN ] SimdIntegerTest.anyTrue 50: [ OK ] SimdIntegerTest.anyTrue (0 ms) 50: [ RUN ] SimdIntegerTest.blend 50: [ OK ] SimdIntegerTest.blend (0 ms) 50: [ RUN ] SimdIntegerTest.cvtB2IB 50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 50: [ RUN ] SimdIntegerTest.cvtIB2B 50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 50: [----------] 23 tests from SimdIntegerTest (0 ms total) 50: 50: [----------] 56 tests from SimdMathTest 50: [ RUN ] SimdMathTest.generateTestPointsFloat 50: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 50: [ RUN ] SimdMathTest.copysign 50: [ OK ] SimdMathTest.copysign (0 ms) 50: [ RUN ] SimdMathTest.invsqrt 50: [ OK ] SimdMathTest.invsqrt (0 ms) 50: [ RUN ] SimdMathTest.maskzInvsqrt 50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPair 50: [ OK ] SimdMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdMathTest.sqrt 50: [ OK ] SimdMathTest.sqrt (0 ms) 50: [ RUN ] SimdMathTest.sqrtUnsafe 50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 50: [ RUN ] SimdMathTest.inv 50: [ OK ] SimdMathTest.inv (0 ms) 50: [ RUN ] SimdMathTest.maskzInv 50: [ OK ] SimdMathTest.maskzInv (0 ms) 50: [ RUN ] SimdMathTest.cbrt 50: [ OK ] SimdMathTest.cbrt (0 ms) 50: [ RUN ] SimdMathTest.invcbrt 50: [ OK ] SimdMathTest.invcbrt (0 ms) 50: [ RUN ] SimdMathTest.log2 50: [ OK ] SimdMathTest.log2 (0 ms) 50: [ RUN ] SimdMathTest.log 50: [ OK ] SimdMathTest.log (0 ms) 50: [ RUN ] SimdMathTest.exp2 50: [ OK ] SimdMathTest.exp2 (0 ms) 50: [ RUN ] SimdMathTest.exp2Unsafe 50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 50: [ RUN ] SimdMathTest.exp 50: [ OK ] SimdMathTest.exp (0 ms) 50: [ RUN ] SimdMathTest.expUnsafe 50: [ OK ] SimdMathTest.expUnsafe (0 ms) 50: [ RUN ] SimdMathTest.pow 50: [ OK ] SimdMathTest.pow (0 ms) 50: [ RUN ] SimdMathTest.powUnsafe 50: [ OK ] SimdMathTest.powUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erf 50: [ OK ] SimdMathTest.erf (0 ms) 50: [ RUN ] SimdMathTest.erfc 50: [ OK ] SimdMathTest.erfc (0 ms) 50: [ RUN ] SimdMathTest.sin 50: [ OK ] SimdMathTest.sin (0 ms) 50: [ RUN ] SimdMathTest.cos 50: [ OK ] SimdMathTest.cos (0 ms) 50: [ RUN ] SimdMathTest.tan 50: [ OK ] SimdMathTest.tan (0 ms) 50: [ RUN ] SimdMathTest.asin 50: [ OK ] SimdMathTest.asin (0 ms) 50: [ RUN ] SimdMathTest.acos 50: [ OK ] SimdMathTest.acos (0 ms) 50: [ RUN ] SimdMathTest.atan 50: [ OK ] SimdMathTest.atan (0 ms) 50: [ RUN ] SimdMathTest.atan2 50: [ OK ] SimdMathTest.atan2 (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrection 50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrection 50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (8 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracy 50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.invSingleAccuracy 50: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cbrtSingleAccuracy 50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.log2SingleAccuracy 50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.logSingleAccuracy 50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracy 50: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracy 50: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracy 50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erfSingleAccuracy 50: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.erfcSingleAccuracy 50: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sinSingleAccuracy 50: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cosSingleAccuracy 50: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.tanSingleAccuracy 50: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.asinSingleAccuracy 50: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.acosSingleAccuracy 50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atanSingleAccuracy 50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atan2SingleAccuracy 50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 56 tests from SimdMathTest (23 ms total) 50: 50: [----------] 1 test from EmptyArrayRefTest 50: [ RUN ] EmptyArrayRefTest.IsEmpty 50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 50: [----------] 1 test from EmptyArrayRefTest (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/0.Assignment 50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/1.Assignment 50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/0.Basic 50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/1.Basic 50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 50: 50: [----------] 3 tests from SimdVectorOperationsTest 50: [ RUN ] SimdVectorOperationsTest.iprod 50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 50: [ RUN ] SimdVectorOperationsTest.norm2 50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 50: [ RUN ] SimdVectorOperationsTest.cprod 50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 50: 50: [----------] 32 tests from Simd4FloatingpointTest 50: [ RUN ] Simd4FloatingpointTest.setZero 50: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 50: [ RUN ] Simd4FloatingpointTest.set 50: [ OK ] Simd4FloatingpointTest.set (0 ms) 50: [ RUN ] Simd4FloatingpointTest.add 50: [ OK ] Simd4FloatingpointTest.add (0 ms) 50: [ RUN ] Simd4FloatingpointTest.sub 50: [ OK ] Simd4FloatingpointTest.sub (0 ms) 50: [ RUN ] Simd4FloatingpointTest.mul 50: [ OK ] Simd4FloatingpointTest.mul (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fma 50: [ OK ] Simd4FloatingpointTest.fma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fms 50: [ OK ] Simd4FloatingpointTest.fms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnma 50: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnms 50: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.abs 50: [ OK ] Simd4FloatingpointTest.abs (0 ms) 50: [ RUN ] Simd4FloatingpointTest.neg 50: [ OK ] Simd4FloatingpointTest.neg (0 ms) 50: [ RUN ] Simd4FloatingpointTest.and 50: [ OK ] Simd4FloatingpointTest.and (0 ms) 50: [ RUN ] Simd4FloatingpointTest.or 50: [ OK ] Simd4FloatingpointTest.or (0 ms) 50: [ RUN ] Simd4FloatingpointTest.xor 50: [ OK ] Simd4FloatingpointTest.xor (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andNot 50: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 50: [ RUN ] Simd4FloatingpointTest.max 50: [ OK ] Simd4FloatingpointTest.max (0 ms) 50: [ RUN ] Simd4FloatingpointTest.min 50: [ OK ] Simd4FloatingpointTest.min (0 ms) 50: [ RUN ] Simd4FloatingpointTest.round 50: [ OK ] Simd4FloatingpointTest.round (0 ms) 50: [ RUN ] Simd4FloatingpointTest.trunc 50: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 50: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 50: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.selectByNotMask 50: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpNe 50: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLe 50: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLt 50: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andB 50: [ OK ] Simd4FloatingpointTest.andB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.orB 50: [ OK ] Simd4FloatingpointTest.orB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.anyTrue 50: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 50: [ RUN ] Simd4FloatingpointTest.blend 50: [ OK ] Simd4FloatingpointTest.blend (0 ms) 50: [ RUN ] Simd4FloatingpointTest.reduce 50: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 50: [ RUN ] Simd4FloatingpointTest.dotProduct 50: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 50: [ RUN ] Simd4FloatingpointTest.transpose 50: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 50: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 50: 50: [----------] 2 tests from Simd4MathTest 50: [ RUN ] Simd4MathTest.invsqrt 50: [ OK ] Simd4MathTest.invsqrt (0 ms) 50: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 50: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 50: [----------] 2 tests from Simd4MathTest (0 ms total) 50: 50: [----------] 1 test from Simd4VectorOperationsTest 50: [ RUN ] Simd4VectorOperationsTest.norm2 50: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 50: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 288 tests from 22 test suites ran. (24 ms total) 50: [ PASSED ] 288 tests. 50/92 Test #50: SimdUnitTests ............................. Passed 0.06 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (0 ms total) 51: [ PASSED ] 9 tests. 51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.02 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (6 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (3 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (10 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (1864 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (908 ms) 52: [----------] 2 tests from GmxChiTest (2869 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (6 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (7 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (0 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (7 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (0 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (7 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (0 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (0 ms) 52: [----------] 10 tests from MindistTest (35 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (7 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (15 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (7 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (53 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (2969 ms total) 52: [ PASSED ] 31 tests. 52/92 Test #52: GmxAnaTest ................................ Passed 3.00 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 260 tests from 16 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (9 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (3 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (8 ms) 53: [----------] 4 tests from GenconfTest (21 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to -1091641229 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (308 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to 1811937231 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (281 ms) 53: [----------] 2 tests from GenionTest (590 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (6 ms) 53: [----------] 1 test from GenRestrTest (6 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 53: Setting the LD random seed to 2147483646 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2112550267 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to 1072662237 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -42111493 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (6 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: Setting the LD random seed to -76570692 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1073740651 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (14 ms) 53: [----------] 3 tests from GromppDirectiveTest (23 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (7 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (8 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (8 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (15 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (29 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (6 ms) 53: [----------] 6 tests from InsertMoleculesTest (76 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (12 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (12 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (27 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (12 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (17 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (11 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (11 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (16 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (14 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (15 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (20 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (5 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [----------] 35 tests from GetIrTest (230 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (14 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (21 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (11 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (12 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (94 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (10 ms) 53: [----------] 6 tests from SolvateTest (164 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) 53: 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (6 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (14 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (5 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (0 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (13 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (16 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (15 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (11 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (8 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (7 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (8 ms) 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest (380 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (10 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (11 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (11 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (3 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (15 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (20 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (3 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (4 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (7 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (8 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (115 ms total) 53: 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: Setting the LD random seed to 232056824 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (23 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: Setting the LD random seed to -156035 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -269353703 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 255846269 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -151266849 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -33778977 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (6 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 1861138281 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 401604479 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -105384195 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1254500354 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: Setting the LD random seed to 2121202942 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (26 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: Setting the LD random seed to -8421542 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -9029677 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (12 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: Setting the LD random seed to -281018633 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: Setting the LD random seed to -204275971 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1610629820 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: Setting the LD random seed to -1610875432 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -99334 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (9 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: Setting the LD random seed to 1576299775 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1115706467 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (10 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: Setting the LD random seed to 1467905279 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -436293969 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Setting the LD random seed to 515880957 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -538402857 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (16 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Setting the LD random seed to -92358705 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1648366055 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: Setting the LD random seed to 1539308526 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -270543649 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (7 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -42075227 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -262147 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -16779417 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -33589379 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Setting the LD random seed to -563101777 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: Setting the LD random seed to 1440465855 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -588259970 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (19 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 53: Setting the LD random seed to -1107364361 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (16 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1058829 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2130700798 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 53: Setting the LD random seed to 2130335734 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (11 ms) 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (253 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 260 tests from 16 test suites ran. (1863 ms total) 53: [ PASSED ] 220 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/92 Test #53: GmxPreprocessTests ........................ Passed 1.89 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (47 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (78 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (57 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (73 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (70 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (130 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (31 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (62 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (114 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (49 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (153 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (109 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1526 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (1527 ms total) 54: [ PASSED ] 30 tests. 54/92 Test #54: Pdb2gmx1Test .............................. Passed 1.54 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (73 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (29 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (31 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (106 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (31 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (35 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (30 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (829 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (72 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (30 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (78 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (31 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (56 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (798 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (1628 ms total) 55: [ PASSED ] 40 tests. 55/92 Test #55: Pdb2gmx2Test .............................. Passed 1.65 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (49 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (121 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (73 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (501 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (108 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (46 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (43 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (95 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (52 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (43 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (109 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (638 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (52 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (21 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (24 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (16 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (188 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (50 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (167 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (76 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (744 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (138 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (1126 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (2515 ms total) 56: [ PASSED ] 39 tests. 56/92 Test #56: Pdb2gmx3Test .............................. Passed 2.54 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (29 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (32 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (55 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (57 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (0 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (33 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (31 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (69 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (1 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (35 ms) 57: [----------] 10 tests from AutocorrTest (347 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (14 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (1 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (1 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (7 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (15 ms) 57: [----------] 10 tests from ExpfitTest (44 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (395 ms total) 57: [ PASSED ] 21 tests. 57/92 Test #57: CorrelationsTest .......................... Passed 0.42 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 58: [----------] 6 tests from AverageModuleTest (2 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 58: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (3 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (3 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (8 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (2 ms) 58: [----------] 3 tests from BinAverageModuleTest (3 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (2 ms) 58: [----------] 3 tests from LifetimeModuleTest (2 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (26 ms total) 58: [ PASSED ] 69 tests. 58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.06 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (16 ms) 59: [----------] 1 test from OutputSelectorDeathTest (16 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (3 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (7 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (4 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (4 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (5 ms) 59: [----------] 5 tests from SetAtomsTest (8 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (5 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (9 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (5 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (6 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (6 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (6 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (16 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (5 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (6 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (84 ms total) 59: [ PASSED ] 67 tests. 59/92 Test #59: CoordinateIOTests ......................... Passed 0.11 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 60: [----------] 11 tests from AngleModuleTest (17 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (4 ms) 60: [----------] 5 tests from ClustsizeTest (9 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (1 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (4 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (4 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (11 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (3 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (15 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (11 ms) 60: [----------] 6 tests from DistanceModuleTest (38 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (17 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (4 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (22 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (47 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (42 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (89 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (4 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -243552609 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (54 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to -100806699 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (39 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -32804 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (18 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -25214977 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (21 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1073872933 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (11 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -1078209102 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (12 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -251682867 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (16 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -287363078 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (16 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 962545631 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (29 ms) 60: [----------] 13 tests from MsdModuleTest (229 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (8 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 60: [----------] 9 tests from PairDistanceModuleTest (18 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (20 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (12 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (12 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (14 ms) 60: [----------] 5 tests from RdfModuleTest (66 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (22 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (6 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) 60: [----------] 5 tests from SasaModuleTest (38 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (6 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (9 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (5 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (3 ms) 60: [----------] 8 tests from SelectModuleTest (30 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (5 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 60: [----------] 10 tests from SurfaceAreaTest (9 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (5 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 60: Setting the LD random seed to 1601564647 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (230 ms) 60: [----------] 4 tests from TopologyInformation (236 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (5 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (6 ms) 60: [----------] 4 tests from TrajectoryModuleTest (14 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (31 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (28 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (29 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (27 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (32 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (28 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (28 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (28 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (28 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (25 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (25 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (17 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (2579 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (13 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (19 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (20 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (16 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (22 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (44 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (44 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (51 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (22 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (23 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (36 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (17 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (19 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (26 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (26 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (11 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (12 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (31 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (23 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (216 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (361 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (365 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (280 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (285 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (254 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (137 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (268 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (294 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (243 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (256 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (54 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (45 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (332 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (386 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (66 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (67 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (158 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (214 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (153 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (75 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (63 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (225 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (221 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (182 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (183 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (78 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (318 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (197 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (86 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (387 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (297 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (599 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (422 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (108 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (289 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (119 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (119 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (236 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (254 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (85 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (76 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (250 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (167 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (321 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (225 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (177 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (133 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (80 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (70 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (204 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (681 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (144 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (161 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (222 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (13734 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (56 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (657 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (25 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (159 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (912 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (18076 ms total) 60: [ PASSED ] 393 tests. 60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 18.12 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (70 ms) 61: [----------] 1 test from DhdlTest (70 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (83 ms) 61: [----------] 1 test from OriresTest (83 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (11 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 61: [----------] 5 tests from EnergyTest (20 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (179 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (83 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (92 ms) 61: [----------] 3 tests from ViscosityTest (356 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (530 ms total) 61: [ PASSED ] 12 tests. 61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.57 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -19925154 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = -19925154 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 46382 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 62: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 62: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 62: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 62: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 62: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 62: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 62: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 62: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 62: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 62: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 62: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 62: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 62: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 62: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 62: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 62: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 62: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 62: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 62: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 62: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 62: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 62: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 62: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 62: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 62: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 62: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 62: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 62: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 62: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 62: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 62: v (156x3): 62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (9 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 62: [----------] 2 tests from DumpTest (10 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 62: [----------] 3 tests from HelpwritingTest (0 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (1 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (12 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (7 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (0 ms) 62: [----------] 7 tests from GmxMakeNdx (24 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -88130053 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 62: [----------] 4 tests from ReportMethodsTest (0 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to 1031396715 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (342 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -69796026 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (459 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -50880533 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (478 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -675430946 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (372 ms) 62: [----------] 4 tests from ConvertTprTest (1653 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -277383314 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (224 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (224 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (4 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (8 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (13 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (20 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (2642 ms total) 62: [ PASSED ] 63 tests. 62/92 Test #62: ToolUnitTests ............................. Passed 2.68 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Setting the LD random seed to -9701405 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (546 ms) 63: [----------] 1 test from ConvertTprTest (546 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 63: Setting the LD random seed to -723795969 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (639 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (639 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (1185 ms total) 63: [ PASSED ] 2 tests. 63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 1.22 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (9 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (9 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 64: [----------] 1 test from StructureIOTest (0 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (0 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (0 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (0 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (30 ms) 64: [----------] 4 tests from MatioTest (30 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 64: [----------] 4 tests from MrcDensityMap (0 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (0 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (46 ms total) 64: [ PASSED ] 421 tests. 64/92 Test #64: FileIOTests ............................... Passed 0.10 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (4 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (11 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (3 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (3 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (15 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (3 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (44 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (3 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (12 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (3 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (3 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (15 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (3 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (4 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (11 ms) 65: [----------] 11 tests from IndexMapTest (60 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (16 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (52 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (12 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (18 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (97 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (203 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (16 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (3 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (3 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (3 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (3 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (3 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 65: [----------] 13 tests from PositionCalculationTest (36 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (18 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (6 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 65: [----------] 33 tests from SelectionCollectionTest (30 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (8 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (6 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (3 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (3 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (37 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (8 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (12 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (11 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (11 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (6 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (8 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (7 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (3 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (6 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (8 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (7 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (11 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (309 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 65: [----------] 17 tests from SelectionOptionTest (2 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 65: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (742 ms total) 65: [ PASSED ] 201 tests. 65/92 Test #65: SelectionUnitTests ........................ Passed 0.80 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (21 ms) 66: [----------] 1 test from MdrunTest (21 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 1966713339 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.5 66: (ns/day) (hour/ns) 66: Performance: 8.516 2.818 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (37 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 2111758334 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 53 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.4 66: (ns/day) (hour/ns) 66: Performance: 9.733 2.466 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (25 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 1541012686 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.019 199.5 66: (ns/day) (hour/ns) 66: Performance: 8.869 2.706 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (46 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (110 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 24 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.252 0.126 199.9 66: (ns/day) (hour/ns) 66: Performance: 11.645 2.061 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (145 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.337 0.176 191.6 66: (ns/day) (hour/ns) 66: Performance: 8.354 2.873 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (225 ms) 66: [----------] 2 tests from Argon12/OutputFiles (371 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -335712339 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.105 0.052 199.8 66: (ns/day) (hour/ns) 66: Performance: 11.545 2.079 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (88 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -423114001 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.098 0.049 199.8 66: (ns/day) (hour/ns) 66: Performance: 12.307 1.950 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (61 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -79691810 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.100 0.050 199.8 66: (ns/day) (hour/ns) 66: Performance: 12.073 1.988 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (68 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (219 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -319652865 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 33 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 199.6 66: (ns/day) (hour/ns) 66: Performance: 9.382 2.558 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (44 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -815868170 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.6 66: (ns/day) (hour/ns) 66: Performance: 10.809 2.220 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (43 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 2104991103 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.5 66: (ns/day) (hour/ns) 66: Performance: 9.920 2.419 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (46 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (134 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (901 ms total) 66: [ PASSED ] 12 tests. 66/92 Test #66: MdrunOutputTests .......................... Passed 0.93 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -545607683 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (59 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.8207725e+03 67: Maximum force = 7.3954834e+03 on atom 2 67: Norm of force = 2.7825089e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1410469889 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (25 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (27 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.4739321e+03 67: Maximum force = 6.1322017e+03 on atom 2 67: Norm of force = 1.7702150e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1078005915 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (39 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (7 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -345124866 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (36 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.7138664e+04 67: Maximum force = 6.7827656e+03 on atom 2 67: Norm of force = 1.9608866e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2077884275 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (32 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: Setting the LD random seed to -1323094163 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (16 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -109200585 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.063 0.032 199.7 67: (ns/day) (hour/ns) 67: Performance: 8.207 2.924 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 34 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.100 0.050 199.8 67: (ns/day) (hour/ns) 67: Performance: 8.654 2.773 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (103 ms) 67: [----------] 9 tests from DensityFittingTest (348 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 61 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.009 0.005 198.8 67: (ns/day) (hour/ns) 67: Performance: 18.207 1.318 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1363177611 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (24 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 19 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.030 0.015 199.6 67: (ns/day) (hour/ns) 67: Performance: 5.710 4.203 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -218152993 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (28 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 60 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.010 0.005 198.9 67: (ns/day) (hour/ns) 67: Performance: 18.059 1.329 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -553652417 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (41 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 17 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.034 0.017 199.6 67: (ns/day) (hour/ns) 67: Performance: 5.028 4.773 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1877384126 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (61 ms) 67: [----------] 4 tests from MimicTest (155 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 41577. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -1887441289 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 37 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.092 0.046 199.7 67: (ns/day) (hour/ns) 67: Performance: 11.240 2.135 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (231 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 59075. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.1977061e+03 67: Maximum force = 1.7794875e+04 on atom 9 67: Norm of force = 7.8732895e+03 67: Setting the LD random seed to -50348043 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (164 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (395 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (942 ms total) 67: [ PASSED ] 15 tests. 67/92 Test #67: MdrunModulesTests ......................... Passed 0.96 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -6324361 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (4 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to 1068945245 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to 2146995947 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: Setting the LD random seed to 2107629303 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (25 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to -1109475396 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (9 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1262485571 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to -562079841 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (12 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: Setting the LD random seed to -134482193 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (8 ms) 68: [----------] 9 tests from GromppTest (85 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1116473113 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 34 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 8.058 2.978 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 38 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 199.6 68: (ns/day) (hour/ns) 68: Performance: 7.482 3.208 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (104 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to 1593833467 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: NOTE: 74 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 5.332 4.501 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 102 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.262 0.631 200.0 68: (ns/day) (hour/ns) 68: Performance: 13.961 1.719 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (674 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -137365577 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 36 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 7.709 3.113 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 43 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.025 199.7 68: (ns/day) (hour/ns) 68: Performance: 10.198 2.353 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 6 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.022 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.538 2.080 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 8 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.305 2.123 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 199.4 68: (ns/day) (hour/ns) 68: Performance: 5.803 4.136 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (165 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1221853317 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 32 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.081 0.040 199.7 68: (ns/day) (hour/ns) 68: Performance: 6.401 3.749 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 32 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.087 0.044 199.8 68: (ns/day) (hour/ns) 68: Performance: 9.872 2.431 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (97 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 1894751118 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.067 0.033 199.7 68: (ns/day) (hour/ns) 68: Performance: 7.748 3.098 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (50 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -33898499 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 31 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.6 68: (ns/day) (hour/ns) 68: Performance: 6.794 3.533 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 199.6 68: (ns/day) (hour/ns) 68: Performance: 10.137 2.367 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (75 ms) 68: [----------] 6 tests from MdrunTerminationTest (1169 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.268 0.134 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.960 2.190 68: trr version: GMX_trn_file (single precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (154 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.352 0.176 200.0 68: (ns/day) (hour/ns) 68: Performance: 8.352 2.874 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (213 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (367 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.283 0.141 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.392 2.309 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.124 0.062 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.486 1.922 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.144 0.072 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.795 2.223 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (333 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.247 0.124 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.879 2.020 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.144 0.072 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.818 2.219 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.138 0.069 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.294 2.125 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (308 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.291 0.145 200.0 68: (ns/day) (hour/ns) 68: Performance: 10.107 2.375 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.168 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.238 2.598 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.154 0.077 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.064 2.385 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (341 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.280 0.140 200.0 68: (ns/day) (hour/ns) 68: Performance: 10.506 2.284 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.160 0.080 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.711 2.471 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.153 0.076 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.177 2.358 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (342 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.242 0.121 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.159 1.974 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.141 0.070 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.051 2.172 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.143 0.071 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.882 2.205 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (314 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.235 0.118 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.483 1.923 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.138 0.069 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.287 2.126 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.133 0.066 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.705 2.050 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (293 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.185 0.092 199.9 68: (ns/day) (hour/ns) 68: Performance: 15.886 1.511 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.109 0.055 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.190 1.691 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.101 0.051 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.389 1.560 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (231 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.114 0.057 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.774 0.931 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 23.944 1.002 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.033 199.7 68: (ns/day) (hour/ns) 68: Performance: 23.395 1.026 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (141 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.141 0.071 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.813 1.153 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.277 1.184 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.425 1.175 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (166 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.058 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.533 0.940 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.222 0.111 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.992 3.433 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.148 0.074 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.493 2.287 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (280 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.322 0.161 200.0 68: (ns/day) (hour/ns) 68: Performance: 9.122 2.631 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.178 0.089 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.739 2.746 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.168 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.269 2.589 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (371 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.341 0.171 200.0 68: (ns/day) (hour/ns) 68: Performance: 8.601 2.790 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.191 0.096 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.126 2.953 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.133 0.066 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.716 2.048 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (381 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.324 0.162 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.067 2.647 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.201 0.101 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.721 3.108 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.168 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.247 2.595 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (431 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.312 0.156 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.413 2.550 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.172 0.086 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.029 2.658 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.160 0.080 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.694 2.476 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (366 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.330 0.165 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.894 2.699 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.206 0.103 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.550 3.179 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.160 0.080 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.744 2.463 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (377 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.320 0.160 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.184 2.613 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.175 0.087 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.899 2.697 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.176 0.088 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.836 2.716 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (362 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.778 0.389 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.775 6.357 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.265 0.133 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.867 4.091 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.303 0.152 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.125 4.683 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (786 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.953 0.477 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.081 7.789 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.531 0.266 199.9 68: (ns/day) (hour/ns) 68: Performance: 2.926 8.203 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.449 0.225 199.9 68: (ns/day) (hour/ns) 68: Performance: 3.460 6.936 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (1126 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.944 0.472 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.111 7.715 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.342 0.171 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.551 5.274 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.292 0.146 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.319 4.512 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (903 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.501 0.251 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.863 4.094 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.268 0.134 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.795 4.141 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.264 0.132 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.898 4.069 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (572 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.423 0.211 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.948 3.454 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.286 0.143 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.428 4.422 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.449 0.225 199.9 68: (ns/day) (hour/ns) 68: Performance: 3.460 6.936 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (657 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.827 0.414 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.550 6.760 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.457 0.228 199.9 68: (ns/day) (hour/ns) 68: Performance: 3.406 7.047 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.450 0.225 199.9 68: (ns/day) (hour/ns) 68: Performance: 3.452 6.953 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (1205 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.824 0.412 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.565 6.732 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.368 0.184 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.222 5.685 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.575 0.288 200.0 68: (ns/day) (hour/ns) 68: Performance: 2.704 8.875 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (966 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.878 0.439 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.344 7.178 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.355 0.178 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.380 5.479 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.360 0.180 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.315 5.561 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (949 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (12214 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.183 0.092 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.009 1.499 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.150 0.075 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.367 2.315 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.101 0.050 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.401 1.558 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (258 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.182 0.091 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.109 1.490 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.103 0.052 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.014 1.598 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.102 0.051 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.281 1.571 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (234 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.240 0.120 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.241 1.961 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.925 2.013 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 33 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.331 0.166 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.689 5.118 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (390 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.531 0.265 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.535 4.336 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.276 0.138 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.625 4.266 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.221 0.111 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.029 3.414 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (621 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.278 0.139 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.580 2.268 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.159 0.080 199.8 68: (ns/day) (hour/ns) 68: Performance: 9.758 2.460 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.192 0.096 199.8 68: (ns/day) (hour/ns) 68: Performance: 8.113 2.958 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (406 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.368 0.184 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.977 3.009 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.214 0.107 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.250 3.311 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.187 0.093 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.326 2.883 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (689 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.466 0.233 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.297 3.811 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.254 0.127 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.127 3.917 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.266 0.133 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.833 4.114 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (622 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.345 0.173 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.501 2.823 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.182 0.091 199.8 68: (ns/day) (hour/ns) 68: Performance: 8.522 2.816 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.181 0.090 199.8 68: (ns/day) (hour/ns) 68: Performance: 8.605 2.789 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (471 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (3695 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.172 0.086 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.044 1.408 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.151 0.076 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.293 2.332 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.141 0.071 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.017 2.179 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (250 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.235 0.118 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.489 1.922 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.133 0.066 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.704 2.051 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.140 0.070 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.067 2.169 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (287 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.251 0.126 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.679 2.055 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 199.1 68: (ns/day) (hour/ns) 68: Performance: 54.394 0.441 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.177 0.088 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.803 2.726 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (359 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.314 0.157 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.361 2.564 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.149 0.074 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.445 2.298 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.110 0.055 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.101 1.702 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (331 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.213 0.106 199.9 68: (ns/day) (hour/ns) 68: Performance: 13.810 1.738 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.124 0.062 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.578 1.908 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.714 1.888 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (265 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.196 0.098 199.9 68: (ns/day) (hour/ns) 68: Performance: 14.987 1.601 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.134 0.067 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.578 2.073 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 199.4 68: (ns/day) (hour/ns) 68: Performance: 34.261 0.701 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (221 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.305 0.152 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.634 2.491 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.182 0.091 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.519 2.817 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.411 2.103 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (343 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.257 0.129 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.422 2.101 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.175 0.088 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.870 2.706 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.170 0.085 199.8 68: (ns/day) (hour/ns) 68: Performance: 9.148 2.623 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (334 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (2393 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.131 0.066 199.8 68: (ns/day) (hour/ns) 68: Performance: 22.367 1.073 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.105 0.053 199.7 68: (ns/day) (hour/ns) 68: Performance: 14.759 1.626 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.110 0.055 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.083 1.704 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (234 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.215 0.108 199.9 68: (ns/day) (hour/ns) 68: Performance: 13.648 1.759 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.124 0.062 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.580 1.908 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.120 0.060 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.998 1.846 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (260 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (495 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.222 0.111 199.9 68: (ns/day) (hour/ns) 68: Performance: 13.199 1.818 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 27 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.119 0.060 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.035 1.841 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.058 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.517 1.776 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (268 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.196 0.098 199.9 68: (ns/day) (hour/ns) 68: Performance: 15.000 1.600 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.110 0.055 199.8 68: (ns/day) (hour/ns) 68: Performance: 14.072 1.706 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.114 0.057 199.7 68: (ns/day) (hour/ns) 68: Performance: 13.605 1.764 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (238 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.145 0.072 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.276 1.184 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 199.6 68: (ns/day) (hour/ns) 68: Performance: 22.504 1.066 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.650 1.162 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (167 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.183 0.092 199.9 68: (ns/day) (hour/ns) 68: Performance: 16.015 1.499 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.113 0.056 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.774 1.742 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.117 0.059 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.263 1.810 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (225 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.323 0.161 200.0 68: (ns/day) (hour/ns) 68: Performance: 9.104 2.636 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.178 0.089 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.731 2.749 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.198 0.099 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.843 3.060 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (383 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.297 0.149 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.879 2.429 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.165 0.083 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.421 2.548 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.166 0.083 199.8 68: (ns/day) (hour/ns) 68: Performance: 9.360 2.564 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (352 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.333 0.167 200.0 68: (ns/day) (hour/ns) 68: Performance: 8.813 2.723 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.179 0.090 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.675 2.766 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.173 0.087 199.8 68: (ns/day) (hour/ns) 68: Performance: 8.986 2.671 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (370 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (2007 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.536 0.268 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.484 4.376 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.276 0.138 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.636 4.258 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.168 0.084 199.8 68: (ns/day) (hour/ns) 68: Performance: 9.265 2.590 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (541 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (541 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.145 0.072 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.273 1.184 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.040 199.7 68: (ns/day) (hour/ns) 68: Performance: 19.557 1.227 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 199.7 68: (ns/day) (hour/ns) 68: Performance: 19.454 1.234 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (174 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.198 0.099 199.9 68: (ns/day) (hour/ns) 68: Performance: 14.837 1.618 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.938 1.506 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.099 0.049 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.753 1.523 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (215 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (390 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to 2138930686 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to 2147335988 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.380 0.190 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.726 3.106 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.131 0.066 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.850 2.025 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.099 0.050 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.650 1.534 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (382 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to 2147147477 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to 1606401919 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.216 0.108 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.584 1.767 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.7 68: (ns/day) (hour/ns) 68: Performance: 12.771 1.879 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.115 0.058 199.7 68: (ns/day) (hour/ns) 68: Performance: 13.492 1.779 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (271 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (654 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.260 0.130 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.316 2.121 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.140 0.070 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.100 2.162 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.134 0.067 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.589 2.071 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (312 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (312 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -8392739 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 199.1 68: (ns/day) (hour/ns) 68: Performance: 12.283 1.954 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (24 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1385465640 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.019 199.6 68: (ns/day) (hour/ns) 68: Performance: 8.888 2.700 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (26 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -153626123 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 199.4 68: (ns/day) (hour/ns) 68: Performance: 8.826 2.719 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (31 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (83 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (24539 ms total) 68: [ PASSED ] 76 tests. 68/92 Test #68: MdrunIOTests .............................. Passed 24.57 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -656507265 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 32 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.654 0.327 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.965 6.053 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.593 0.297 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.366 5.497 69: [ OK ] CompelTest.SwapCanRun (1378 ms) 69: [----------] 1 test from CompelTest (1378 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 72 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.019 0.010 199.4 69: (ns/day) (hour/ns) 69: Performance: 8.858 2.709 69: Setting the LD random seed to -50366856 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalBondWorks (30 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 88 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.043 0.022 199.7 69: (ns/day) (hour/ns) 69: Performance: 3.968 6.049 69: Setting the LD random seed to -1610745859 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (56 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.029 0.015 199.6 69: (ns/day) (hour/ns) 69: Performance: 5.934 4.045 69: Setting the LD random seed to -1141200194 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (36 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 71 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.019 0.010 199.4 69: (ns/day) (hour/ns) 69: Performance: 8.958 2.679 69: Setting the LD random seed to -144790533 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (22 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 24 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.024 0.012 199.3 69: (ns/day) (hour/ns) 69: Performance: 7.171 3.347 69: Setting the LD random seed to -420092425 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (19 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 72 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.020 0.010 199.4 69: (ns/day) (hour/ns) 69: Performance: 8.641 2.777 69: Setting the LD random seed to -8201 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (20 ms) 69: [----------] 6 tests from BondedInteractionsTest (185 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: 69: NOTE: 42 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.015 0.007 198.6 69: (ns/day) (hour/ns) 69: Performance: 23.397 1.026 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -44057089 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to 2147444151 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (27 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: Setting the LD random seed to -43134582 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.23 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 11 % of the run time was spent in domain decomposition, 69: 3 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.695 0.347 200.0 69: (ns/day) (hour/ns) 69: Performance: 10.447 2.297 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (3986 ms) 69: [----------] 2 tests from BoxDeformationTest (4013 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to 1879048187 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.810 0.405 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.691 5.116 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (626 ms) 69: [----------] 1 test from PositionRestraintCommTest (626 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 1868541534 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 19 % of the run time was spent in domain decomposition, 69: 11 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.318 0.159 199.9 69: (ns/day) (hour/ns) 69: Performance: 2.714 8.845 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -134220549 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 18 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.099 0.050 199.8 69: (ns/day) (hour/ns) 69: Performance: 8.697 2.760 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (57428 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -1082961929 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 14 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.103 0.052 199.8 69: (ns/day) (hour/ns) 69: Performance: 8.365 2.869 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -273219715 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.95 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.096 0.048 199.8 69: (ns/day) (hour/ns) 69: Performance: 8.974 2.674 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (151 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (57580 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 2133834715 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.043 0.022 199.5 69: (ns/day) (hour/ns) 69: Performance: 20.026 1.198 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -16885203 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.048 0.024 199.5 69: (ns/day) (hour/ns) 69: Performance: 17.865 1.343 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (64 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (64 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.091 0.045 199.8 69: (ns/day) (hour/ns) 69: Performance: 17.092 1.404 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (59 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.094 0.047 199.7 69: (ns/day) (hour/ns) 69: Performance: 16.518 1.453 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (62 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.093 0.046 199.7 69: (ns/day) (hour/ns) 69: Performance: 16.739 1.434 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (61 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.120 0.060 199.8 69: (ns/day) (hour/ns) 69: Performance: 12.996 1.847 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (74 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.122 0.061 199.8 69: (ns/day) (hour/ns) 69: Performance: 12.694 1.891 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (76 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.110 0.055 199.8 69: (ns/day) (hour/ns) 69: Performance: 14.105 1.702 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (72 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.112 0.056 199.8 69: (ns/day) (hour/ns) 69: Performance: 13.877 1.730 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (73 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.144 0.072 199.8 69: (ns/day) (hour/ns) 69: Performance: 10.788 2.225 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (89 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.193 0.097 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.052 2.981 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (161 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.208 0.104 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.474 3.211 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (185 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 25 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.128 0.064 199.8 69: (ns/day) (hour/ns) 69: Performance: 12.109 1.982 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (133 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1049 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -269404395 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 16 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.6 69: (ns/day) (hour/ns) 69: Performance: 43.150 0.556 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (43 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -68449 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.069 0.034 199.7 69: (ns/day) (hour/ns) 69: Performance: 45.201 0.531 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (41 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -1142685779 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.094 0.047 199.7 69: (ns/day) (hour/ns) 69: Performance: 32.897 0.730 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (54 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -71304729 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.091 0.046 199.7 69: (ns/day) (hour/ns) 69: Performance: 34.152 0.703 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (52 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (191 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (65200 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/92 Test #69: MdrunTestsOneRank ......................... Passed 65.22 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Generating 1-4 interactions: fudge = 0.5 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -280681 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 2.5%. 70: The balanceable part of the MD step is 14%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.4%. 70: 70: 70: NOTE: 39 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.512 0.628 399.9 70: (ns/day) (hour/ns) 70: Performance: 2.063 11.632 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.611 0.403 399.9 70: (ns/day) (hour/ns) 70: Performance: 3.217 7.461 70: [ OK ] CompelTest.SwapCanRun (2463 ms) 70: [----------] 1 test from CompelTest (2463 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 66 % of the run time was spent in domain decomposition, 70: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.285 0.071 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.212 19.799 70: Setting the LD random seed to -85211377 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalBondWorks (227 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 80 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.392 0.366 380.4 70: (ns/day) (hour/ns) 70: Performance: 0.236 101.676 70: Setting the LD random seed to -1612730693 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (1376 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 73 % of the run time was spent in domain decomposition, 70: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.468 0.117 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.738 32.530 70: Setting the LD random seed to -1814339842 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (222 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 52 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.556 0.139 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.621 38.628 70: Setting the LD random seed to 1069544954 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (317 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 48 % of the run time was spent in domain decomposition, 70: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 15 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.377 0.094 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.917 26.174 70: Setting the LD random seed to -671942707 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (159 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 80 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 9 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.649 0.412 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.209 114.567 70: Setting the LD random seed to -35915777 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (995 ms) 70: [----------] 6 tests from BondedInteractionsTest (3299 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 60 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 7 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.371 0.120 308.5 70: (ns/day) (hour/ns) 70: Performance: 1.436 16.712 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -545263622 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to -545540129 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (501 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: Setting the LD random seed to -176685225 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.23 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 12.2%. 70: The balanceable part of the MD step is 13%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.6%. 70: 70: 70: NOTE: 16 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 5.955 1.489 400.0 70: (ns/day) (hour/ns) 70: Performance: 2.437 9.847 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (5683 ms) 70: [----------] 2 tests from BoxDeformationTest (6185 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: Setting the LD random seed to -37748961 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.400 0.350 399.9 70: (ns/day) (hour/ns) 70: Performance: 5.429 4.420 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1308 ms) 70: [----------] 1 test from PositionRestraintCommTest (1308 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -1191184449 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 8 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.080 0.520 399.9 70: (ns/day) (hour/ns) 70: Performance: 0.831 28.888 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -369893417 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.949 0.237 399.9 70: (ns/day) (hour/ns) 70: Performance: 1.820 13.187 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (46038 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1945350823 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 7 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.528 0.920 383.4 70: (ns/day) (hour/ns) 70: Performance: 0.469 51.125 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -1082282001 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.95 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.568 0.142 399.7 70: (ns/day) (hour/ns) 70: Performance: 3.039 7.897 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (2321 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (48360 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 2027945961 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.399 0.636 377.4 70: (ns/day) (hour/ns) 70: Performance: 0.679 35.323 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -805607945 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.095 0.556 377.0 70: (ns/day) (hour/ns) 70: Performance: 0.777 30.877 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2908 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2908 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 8.0%. 70: The balanceable part of the MD step is 53%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 4.2%. 70: 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 16 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.812 0.453 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.715 13.991 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1438 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 24.3%. 70: The balanceable part of the MD step is 43%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 10.5%. 70: 70: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 26 % of the run time was spent in domain decomposition, 70: 7 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.571 0.143 399.2 70: (ns/day) (hour/ns) 70: Performance: 5.435 4.416 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (305 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 20.3%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 8.1%. 70: 70: NOTE: 8.1 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 26 % of the run time was spent in domain decomposition, 70: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.515 0.129 399.4 70: (ns/day) (hour/ns) 70: Performance: 6.031 3.979 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (735 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 10.6%. 70: The balanceable part of the MD step is 52%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 5.5%. 70: 70: NOTE: 5.5 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 9 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.501 0.125 399.7 70: (ns/day) (hour/ns) 70: Performance: 6.207 3.867 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (788 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.9%. 70: The balanceable part of the MD step is 49%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 3.4%. 70: 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 6 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.530 0.133 399.8 70: (ns/day) (hour/ns) 70: Performance: 5.866 4.091 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (232 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 70: Parrinello-Rahman is not implemented in md-vv. 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.523 0.146 357.5 70: (ns/day) (hour/ns) 70: Performance: 5.314 4.516 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (311 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 31 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.548 0.137 399.2 70: (ns/day) (hour/ns) 70: Performance: 5.662 4.239 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (237 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 7 % of the run time was spent in domain decomposition, 70: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.472 0.119 398.6 70: (ns/day) (hour/ns) 70: Performance: 6.560 3.658 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (246 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.538 0.139 387.1 70: (ns/day) (hour/ns) 70: Performance: 5.597 4.288 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (263 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 26 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.303 0.076 399.6 70: (ns/day) (hour/ns) 70: Performance: 10.255 2.340 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (199 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.376 0.094 399.2 70: (ns/day) (hour/ns) 70: Performance: 8.262 2.905 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (292 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (5052 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -562037890 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 55%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 9 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.315 0.079 399.7 70: (ns/day) (hour/ns) 70: Performance: 19.760 1.215 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (172 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -402735125 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 9.8%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 4.5%. 70: 70: 70: NOTE: 23 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.331 0.083 399.7 70: (ns/day) (hour/ns) 70: Performance: 18.751 1.280 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (156 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -212091138 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 52%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 21 % of the run time was spent in domain decomposition, 70: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.355 0.089 399.7 70: (ns/day) (hour/ns) 70: Performance: 17.508 1.371 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (184 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -68330761 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.0%. 70: The balanceable part of the MD step is 55%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.0%. 70: 70: 70: NOTE: 15 % of the run time was spent in domain decomposition, 70: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.384 0.096 399.7 70: (ns/day) (hour/ns) 70: Performance: 16.167 1.484 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (231 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (744 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (70403 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 70.42 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to -553666165 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.957 1.479 200.0 71: (ns/day) (hour/ns) 71: Performance: 23.490 1.022 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (1514 ms) 71: [----------] 1 test from DispersionCorrectionTest (1514 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 71: 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to -1073742337 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.111 0.055 199.8 71: (ns/day) (hour/ns) 71: Performance: 34.271 0.700 71: [ OK ] OriresTest.OriresCanRun (528 ms) 71: [----------] 1 test from OriresTest (528 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to 2063433343 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.251 0.126 199.9 71: (ns/day) (hour/ns) 71: Performance: 36.070 0.665 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (60480 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -4198945 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.567 0.283 200.0 71: (ns/day) (hour/ns) 71: Performance: 16.010 1.499 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (23093 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (83574 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (85642 ms total) 71: [ PASSED ] 5 tests. 71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 85.66 sec test 72 Start 72: Minimize1RankTests 72: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.7990997e+01 72: Maximum force = 1.8629692e+02 on atom 13 72: Norm of force = 8.7721836e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (197 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.5862350e+01 72: Maximum force = 4.2726685e+02 on atom 13 72: Norm of force = 1.8452681e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (198 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1937723e+02 72: Maximum force = 9.9988691e+03 on atom 9 72: Norm of force = 4.6167015e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (85 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5174414e+02 72: Maximum force = 7.4208760e+03 on atom 9 72: Norm of force = 3.5692977e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (92 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.5698444e+02 72: Maximum force = 4.5702216e+02 on atom 17 72: Norm of force = 1.8327095e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (77 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06799e+03 on atom 28 72: F-Norm = 4.26914e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.6941290e+02 72: Maximum force = 2.1840109e+02 on atom 17 72: Norm of force = 7.9232004e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (121 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (773 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.7425687e-01 72: Maximum force = 4.0132279e+00 on atom 1 72: Norm of force = 1.6383933e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (12 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (13 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1939673e+02 72: Maximum force = 9.9704229e+03 on atom 9 72: Norm of force = 4.6227534e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (93 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5625757e+02 72: Maximum force = 7.5018242e+03 on atom 9 72: Norm of force = 3.6139019e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (85 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: Double precision normally gives you higher accuracy, but this is often not 72: needed for preparing to run molecular dynamics. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.6111609e+02 72: Maximum force = 1.2685385e+04 on atom 10 72: Norm of force = 6.0643598e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (81 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (300 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (1088 ms total) 72: [ PASSED ] 12 tests. 72/92 Test #72: Minimize1RankTests ........................ Passed 1.10 sec test 73 Start 73: Minimize2RankTests 73: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.7990952e+01 73: Maximum force = 1.8629709e+02 on atom 13 73: Norm of force = 8.7721970e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (407 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.5862202e+01 73: Maximum force = 4.2727243e+02 on atom 13 73: Norm of force = 1.8452909e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (520 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1937720e+02 73: Maximum force = 9.9988691e+03 on atom 9 73: Norm of force = 4.6167015e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (168 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5174358e+02 73: Maximum force = 7.4208833e+03 on atom 9 73: Norm of force = 3.5692986e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (628 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.5698444e+02 73: Maximum force = 4.5702222e+02 on atom 17 73: Norm of force = 1.8327095e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (406 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06799e+03 on atom 28 73: F-Norm = 4.26914e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.6941266e+02 73: Maximum force = 2.1838609e+02 on atom 17 73: Norm of force = 7.9233324e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (391 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2523 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.7425687e-01 73: Maximum force = 4.0132279e+00 on atom 3 73: Norm of force = 1.6383933e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (280 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.9064195e-01 73: Maximum force = 2.5781672e+00 on atom 3 73: Norm of force = 1.0525324e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (1164 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1939664e+02 73: Maximum force = 9.9704229e+03 on atom 9 73: Norm of force = 4.6227537e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (385 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5625771e+02 73: Maximum force = 7.5018237e+03 on atom 9 73: Norm of force = 3.6139019e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (631 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (102 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (2567 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (5117 ms total) 73: [ PASSED ] 12 tests. 73/92 Test #73: Minimize2RankTests ........................ Passed 5.15 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 46 tests from 3 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: SIMD width: 4 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. 4xM 0.117 0.1171 10.1633 5.3768 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (35 ms) 74: [----------] 1 test from NonbondedBenchTest (35 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 198.1 74: (ns/day) (hour/ns) 74: Performance: 234.654 0.102 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (single precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.126 0.063 199.9 74: (ns/day) (hour/ns) 74: Performance: 23.327 1.029 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (129 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 24 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.219 1.480 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.033 199.8 74: (ns/day) (hour/ns) 74: Performance: 43.888 0.547 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (136 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.177 0.089 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.547 1.450 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 57 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.050 0.025 199.8 74: (ns/day) (hour/ns) 74: Performance: 58.111 0.413 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (125 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.122 0.061 199.9 74: (ns/day) (hour/ns) 74: Performance: 24.089 0.996 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 58 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.051 0.026 199.8 74: (ns/day) (hour/ns) 74: Performance: 57.194 0.420 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (98 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.008 0.004 197.1 74: (ns/day) (hour/ns) 74: Performance: 381.650 0.063 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 46 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.072 0.036 199.8 74: (ns/day) (hour/ns) 74: Performance: 40.820 0.588 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (368 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.413 0.206 200.0 74: (ns/day) (hour/ns) 74: Performance: 7.120 3.371 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.091 0.045 199.9 74: (ns/day) (hour/ns) 74: Performance: 32.324 0.742 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (724 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.225 0.113 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.035 1.841 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 37 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.100 0.050 199.9 74: (ns/day) (hour/ns) 74: Performance: 29.495 0.814 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (429 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.351 0.176 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.363 2.870 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 71 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.114 0.057 199.9 74: (ns/day) (hour/ns) 74: Performance: 25.699 0.934 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (640 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.751 0.376 200.0 74: (ns/day) (hour/ns) 74: Performance: 3.911 6.136 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.066 0.033 199.8 74: (ns/day) (hour/ns) 74: Performance: 44.667 0.537 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (496 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.633 0.317 200.0 74: (ns/day) (hour/ns) 74: Performance: 4.639 5.173 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.097 0.048 199.9 74: (ns/day) (hour/ns) 74: Performance: 30.286 0.792 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (402 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.422 0.211 199.9 74: (ns/day) (hour/ns) 74: Performance: 6.954 3.451 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.068 0.034 199.8 74: (ns/day) (hour/ns) 74: Performance: 42.897 0.559 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (335 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.745 0.373 200.0 74: (ns/day) (hour/ns) 74: Performance: 3.941 6.089 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 46 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.091 0.046 199.8 74: (ns/day) (hour/ns) 74: Performance: 32.270 0.744 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (470 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (4358 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.186 0.093 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.822 1.517 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 54 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.037 0.500 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (157 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.187 0.093 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.731 1.526 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 54 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.033 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.112 0.532 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (147 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.195 0.097 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.085 1.591 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.393 0.486 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (148 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.198 0.099 199.9 74: (ns/day) (hour/ns) 74: Performance: 14.799 1.622 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.6 74: (ns/day) (hour/ns) 74: Performance: 49.130 0.489 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (150 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.308 0.154 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.535 2.517 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 72 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.096 0.048 199.8 74: (ns/day) (hour/ns) 74: Performance: 30.621 0.784 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (230 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.223 0.112 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.158 1.824 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.964 0.480 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.201 1.481 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.754 0.482 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.182 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.162 1.485 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.341 0.486 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.205 1.481 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.673 0.483 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.217 1.480 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.249 0.487 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.182 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.143 1.487 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.261 0.487 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (141 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.229 0.115 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.827 1.871 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.629 0.484 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (161 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.247 0.123 199.9 74: (ns/day) (hour/ns) 74: Performance: 11.895 2.018 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.076 0.038 199.8 74: (ns/day) (hour/ns) 74: Performance: 38.545 0.623 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (179 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.002 196.9 74: (ns/day) (hour/ns) 74: Performance: 813.172 0.030 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 44 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.075 0.038 199.8 74: (ns/day) (hour/ns) 74: Performance: 39.153 0.613 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (55 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.230 0.115 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.762 1.881 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.443 0.485 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (170 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.234 0.117 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.553 1.912 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.745 0.482 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (164 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.234 0.117 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.559 1.911 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.594 0.484 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (164 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.235 0.118 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.486 1.922 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.059 0.029 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.848 0.481 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (165 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.236 0.118 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.449 1.928 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 57 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.033 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.122 0.532 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (169 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.247 0.124 199.9 74: (ns/day) (hour/ns) 74: Performance: 11.884 2.020 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.934 0.490 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.306 0.153 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.590 2.503 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 37 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.089 0.044 199.8 74: (ns/day) (hour/ns) 74: Performance: 33.141 0.724 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (246 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.234 0.117 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.549 1.912 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 54 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.199 0.498 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (175 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.283 0.142 199.9 74: (ns/day) (hour/ns) 74: Performance: 10.378 2.313 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.063 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 46.814 0.513 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (201 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.216 0.108 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.598 1.765 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 46 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.096 0.048 199.8 74: (ns/day) (hour/ns) 74: Performance: 30.559 0.785 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (183 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.298 0.149 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.855 2.435 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 48 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.077 0.038 199.7 74: (ns/day) (hour/ns) 74: Performance: 38.278 0.627 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (224 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.223 0.112 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.146 1.826 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 49 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.067 0.033 199.7 74: (ns/day) (hour/ns) 74: Performance: 43.850 0.547 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.276 0.138 199.9 74: (ns/day) (hour/ns) 74: Performance: 10.631 2.257 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.135 0.067 199.9 74: (ns/day) (hour/ns) 74: Performance: 21.788 1.102 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (232 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.417 0.209 199.9 74: (ns/day) (hour/ns) 74: Performance: 7.044 3.407 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 58 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.120 0.060 199.8 74: (ns/day) (hour/ns) 74: Performance: 24.421 0.983 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (325 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.509 0.255 199.9 74: (ns/day) (hour/ns) 74: Performance: 5.770 4.160 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.033 199.7 74: (ns/day) (hour/ns) 74: Performance: 44.822 0.535 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (348 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.224 0.112 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.119 1.829 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.090 0.045 199.8 74: (ns/day) (hour/ns) 74: Performance: 32.426 0.740 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (188 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.315 0.158 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.314 2.577 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 46 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.079 0.039 199.7 74: (ns/day) (hour/ns) 74: Performance: 37.219 0.645 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (237 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.310 0.155 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.471 2.534 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 40 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.028 0.014 199.4 74: (ns/day) (hour/ns) 74: Performance: 104.621 0.229 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (204 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.006 197.7 74: (ns/day) (hour/ns) 74: Performance: 243.984 0.098 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 62 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.120 0.060 199.8 74: (ns/day) (hour/ns) 74: Performance: 24.448 0.982 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (118 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5986 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 46 tests from 3 test suites ran. (10411 ms total) 74: [ PASSED ] 46 tests. 74/92 Test #74: MdrunNonIntegratorTests ................... Passed 10.45 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (321 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (185 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (163 ms) 75: [----------] 3 tests from Simple/TpiTest (671 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (690 ms total) 75: [ PASSED ] 3 tests. 75/92 Test #75: MdrunTpiTests ............................. Passed 0.72 sec test 76 Start 76: MdrunMpiTests 76: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 47 % of the run time was spent in domain decomposition, 76: 21 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.090 0.022 399.6 76: (ns/day) (hour/ns) 76: Performance: 3.849 6.236 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1865543383 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.OneQuantumMol (122 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 34 % of the run time was spent in domain decomposition, 76: 21 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 18 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.088 0.022 399.4 76: (ns/day) (hour/ns) 76: Performance: 3.921 6.121 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 950987599 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.AllQuantumMol (95 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 59 % of the run time was spent in domain decomposition, 76: 20 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.172 0.043 399.8 76: (ns/day) (hour/ns) 76: Performance: 2.011 11.932 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -419840389 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.TwoQuantumMol (408 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 61 % of the run time was spent in domain decomposition, 76: 24 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.094 0.024 399.6 76: (ns/day) (hour/ns) 76: Performance: 3.660 6.557 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -6316291 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.BondCuts (131 ms) 76: [----------] 4 tests from MimicTest (758 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: Setting the LD random seed to -2817 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -1074016782 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -84607536 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 1809767423 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 27.8%. 76: The balanceable part of the MD step is 44%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 12.2%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: NOTE: 12.2 % of the available CPU time was lost due to load imbalance 76: in the domain decomposition. 76: You can consider manually changing the decomposition (option -dd); 76: e.g. by using fewer domains along the box dimension in which there is 76: considerable inhomogeneity in the simulated system. 76: 76: NOTE: 21 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 11 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.161 0.291 399.6 76: (ns/day) (hour/ns) 76: Performance: 6.243 3.844 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (379 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.654 0.164 399.9 76: (ns/day) (hour/ns) 76: Performance: 11.094 2.163 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (221 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.6%. 76: The balanceable part of the MD step is 28%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.4%. 76: 76: 76: NOTE: 11 % of the run time was spent in domain decomposition, 76: 5 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.451 0.363 399.8 76: (ns/day) (hour/ns) 76: Performance: 4.999 4.801 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (13346 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.618 0.155 399.1 76: (ns/day) (hour/ns) 76: Performance: 11.713 2.049 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (8085 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.974 0.244 399.9 76: (ns/day) (hour/ns) 76: Performance: 7.446 3.223 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (396 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.557 0.394 395.3 76: (ns/day) (hour/ns) 76: Performance: 4.607 5.210 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (766 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (23195 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (23990 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/92 Test #76: MdrunMpiTests ............................. Passed 24.02 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 2 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 2 tests from 1 test suite ran. (15 ms total) 77: [ PASSED ] 2 tests. 77: 77: YOU HAVE 4 DISABLED TESTS 77: 77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.04 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (16 ms total) 78: [ PASSED ] 1 test. 78: 78: YOU HAVE 4 DISABLED TESTS 78: 78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 0 tests from 0 test suites. 79: [==========] 0 tests from 0 test suites ran. (0 ms total) 79: [ PASSED ] 0 tests. 79: 79: YOU HAVE 10 DISABLED TESTS 79: 79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Setting the LD random seed to -604571911 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to 2045706046 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.523 0.262 200.0 80: (ns/day) (hour/ns) 80: Performance: 6.937 3.460 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (14440 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.416 0.208 200.0 80: (ns/day) (hour/ns) 80: Performance: 8.730 2.749 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (225 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 26 % of the run time was spent in domain decomposition, 80: 20 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.094 0.047 199.7 80: (ns/day) (hour/ns) 80: Performance: 1.844 13.017 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (54949 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.775 0.387 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.682 5.126 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (414 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (70030 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (70056 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 70.08 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: Setting the LD random seed to 2130664575 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Setting the LD random seed to -1099431953 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 7.1%. 81: The balanceable part of the MD step is 30%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.1%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.534 0.383 399.9 81: (ns/day) (hour/ns) 81: Performance: 4.731 5.073 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (24725 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 11.6%. 81: The balanceable part of the MD step is 25%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.9%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 3 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.536 0.384 399.9 81: (ns/day) (hour/ns) 81: Performance: 4.725 5.080 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (579 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 19 % of the run time was spent in domain decomposition, 81: 10 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 9 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.154 0.039 399.1 81: (ns/day) (hour/ns) 81: Performance: 2.235 10.739 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (42838 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.888 0.223 398.7 81: (ns/day) (hour/ns) 81: Performance: 8.149 2.945 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (7546 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.457 0.365 399.3 81: (ns/day) (hour/ns) 81: Performance: 4.971 4.828 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (1047 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 19 % of the run time was spent in domain decomposition, 81: 19 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.061 0.016 393.6 81: (ns/day) (hour/ns) 81: Performance: 5.547 4.327 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (26750 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 15.6%. 81: The balanceable part of the MD step is 32%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 5.0%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.314 0.328 399.9 81: (ns/day) (hour/ns) 81: Performance: 5.524 4.345 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (467 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (103957 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (103983 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 104.01 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 98.1 82: (ns/day) (hour/ns) 82: Performance: 934.698 0.026 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 96.1 82: (ns/day) (hour/ns) 82: Performance: 2297.015 0.010 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.9 82: (ns/day) (hour/ns) 82: Performance: 2744.140 0.009 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2512.477 0.010 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2559.449 0.009 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.4 82: (ns/day) (hour/ns) 82: Performance: 2482.109 0.010 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (34 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (34 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (44 ms total) 82: [ PASSED ] 1 test. 82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.07 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.5%. 83: 83: 83: NOTE: 36 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.003 0.002 195.5 83: (ns/day) (hour/ns) 83: Performance: 836.469 0.029 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 20.2%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 10.5%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 17 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.220 0.610 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.408 9.969 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 11 % of the run time was spent in domain decomposition, 83: 5 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 27 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.9 83: (ns/day) (hour/ns) 83: Performance: 1917.993 0.013 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 18.6%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 9.3%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 9.3 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 13 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.627 0.313 200.0 83: (ns/day) (hour/ns) 83: Performance: 4.687 5.121 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 189.8 83: (ns/day) (hour/ns) 83: Performance: 1959.165 0.012 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.002 0.001 183.1 83: (ns/day) (hour/ns) 83: Performance: 1787.493 0.013 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2693 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2693 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (2700 ms total) 83: [ PASSED ] 1 test. 83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 2.72 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.1 84: (ns/day) (hour/ns) 84: Performance: 1009.106 0.024 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2382.287 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2868.060 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2846.855 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2715.114 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2845.540 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (46 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1799.239 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2374.940 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2848.171 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2709.144 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2694.923 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2703.200 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 2060.399 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2370.371 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2935.014 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2722.313 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2739.259 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2673.869 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 2052.847 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2400.855 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2916.948 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2739.259 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2046.709 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2540.451 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1695.265 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 79.5 84: (ns/day) (hour/ns) 84: Performance: 1957.608 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1963.223 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1922.782 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1814.074 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1832.419 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1385.649 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2386.902 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2916.948 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2796.457 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2753.953 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2788.861 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 2056.273 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2412.135 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.000 95.2 84: (ns/day) (hour/ns) 84: Performance: 2957.558 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2736.825 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2771.297 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2783.820 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 2054.216 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2386.902 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2797.726 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 60.6 84: (ns/day) (hour/ns) 84: Performance: 1700.412 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1612.721 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1668.633 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1440.064 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: NOTE: 36 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1595.595 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.000 94.9 84: (ns/day) (hour/ns) 84: Performance: 3052.821 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2738.042 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2785.079 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2842.914 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 2021.192 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2436.944 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.000 95.1 84: (ns/day) (hour/ns) 84: Performance: 2946.243 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2795.188 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2734.396 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2723.516 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1390.653 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2408.363 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2903.202 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2721.110 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2775.042 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2768.806 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (26 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 2050.797 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2392.464 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2922.483 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2763.837 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2710.336 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2771.297 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1928.198 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 2538.358 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2921.097 0.008 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.000 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2814.342 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2795.188 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2793.920 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1943.405 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1703.704 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2687.868 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2655.428 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2648.579 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2611.528 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 2010.638 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 2322.999 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2778.797 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2580.894 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2678.519 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2668.079 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 2033.199 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 2331.792 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 2807.928 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2627.119 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2648.579 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2618.187 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (24 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.8 84: (ns/day) (hour/ns) 84: Performance: 1683.222 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.1 84: (ns/day) (hour/ns) 84: Performance: 1333.751 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.0 84: (ns/day) (hour/ns) 84: Performance: 1631.513 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.3 84: (ns/day) (hour/ns) 84: Performance: 1448.870 0.017 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 2106.186 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.7 84: (ns/day) (hour/ns) 84: Performance: 1999.544 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.0 84: (ns/day) (hour/ns) 84: Performance: 1650.306 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.8 84: (ns/day) (hour/ns) 84: Performance: 1763.192 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 2105.466 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1958.853 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.6 84: (ns/day) (hour/ns) 84: Performance: 1874.800 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1953.883 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.9 84: (ns/day) (hour/ns) 84: Performance: 1663.227 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.9 84: (ns/day) (hour/ns) 84: Performance: 1817.284 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 2084.098 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1871.383 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.8 84: (ns/day) (hour/ns) 84: Performance: 1882.822 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.7 84: (ns/day) (hour/ns) 84: Performance: 1903.180 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1420.146 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1573.587 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1750.666 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1980.898 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1984.727 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 2041.960 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1655.629 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1816.213 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 2004.749 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1945.860 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1949.555 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1977.719 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (25 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1311.323 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1223.554 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 2056.960 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1970.759 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1986.007 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1968.870 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (26 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1447.508 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1565.589 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1744.716 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1392.539 0.017 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 98.2 84: (ns/day) (hour/ns) 84: Performance: 1150.438 0.021 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1635.845 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (27 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1117.467 0.021 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1172.107 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1256.495 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1055.800 0.023 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1253.937 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1263.971 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1364.170 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1470.660 0.016 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1358.455 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1290.717 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1585.330 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1590.652 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (27 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (661 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (672 ms total) 84: [ PASSED ] 25 tests. 84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 0.70 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 194.8 85: (ns/day) (hour/ns) 85: Performance: 864.281 0.028 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.8 85: (ns/day) (hour/ns) 85: Performance: 1898.488 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.7%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 2265.757 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.6%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2135.388 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1706.063 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 2170.752 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (863 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 17.3%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 15 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 36 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.768 0.384 200.0 85: (ns/day) (hour/ns) 85: Performance: 3.825 6.274 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1909.669 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2086.569 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1986.968 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1993.075 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1971.075 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1297 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 24 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1570.578 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1802.134 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 1995.334 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1964.162 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 2013.924 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1973.284 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (163 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1601.818 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.4 85: (ns/day) (hour/ns) 85: Performance: 1881.959 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 2057.303 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 18.5%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 9.1%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 9.1 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 16 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.644 0.848 193.9 85: (ns/day) (hour/ns) 85: Performance: 1.733 13.852 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 2011.951 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 2023.848 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1880 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.2 85: (ns/day) (hour/ns) 85: Performance: 1847.531 0.013 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 2042.637 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.736 0.384 191.7 85: (ns/day) (hour/ns) 85: Performance: 3.827 6.271 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2195.899 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.5 85: (ns/day) (hour/ns) 85: Performance: 2262.429 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 2259.525 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1239 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1736.112 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 2005.075 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 2200.605 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.924 0.994 193.6 85: (ns/day) (hour/ns) 85: Performance: 1.478 16.241 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.080 0.556 194.3 85: (ns/day) (hour/ns) 85: Performance: 2.642 9.084 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2046.369 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3448 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1685.756 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1961.973 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.7 85: (ns/day) (hour/ns) 85: Performance: 2203.754 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.6 85: (ns/day) (hour/ns) 85: Performance: 2044.671 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1900.831 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 2120.321 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (383 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.309 0.655 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.244 10.696 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.928 0.480 193.3 85: (ns/day) (hour/ns) 85: Performance: 3.060 7.842 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 2279.169 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2228.869 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2178.428 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2114.136 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2593 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1803.189 0.013 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2052.847 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2382.748 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2246.342 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2290.184 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 2257.868 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (154 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.7 85: (ns/day) (hour/ns) 85: Performance: 1723.484 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 59 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.260 0.654 192.7 85: (ns/day) (hour/ns) 85: Performance: 2.246 10.685 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2353.617 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2103.669 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2243.071 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2137.982 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1696 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.148 0.574 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.558 9.381 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 2076.371 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 2281.701 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 2148.045 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 2143.934 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 2114.499 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1383 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1751.662 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2047.049 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2282.124 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 2148.045 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 53 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.436 0.734 195.6 85: (ns/day) (hour/ns) 85: Performance: 2.001 11.993 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 2127.277 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1786 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.9 85: (ns/day) (hour/ns) 85: Performance: 1764.202 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 191.5 85: (ns/day) (hour/ns) 85: Performance: 2015.901 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2388.290 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 183.6 85: (ns/day) (hour/ns) 85: Performance: 2208.494 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.2 85: (ns/day) (hour/ns) 85: Performance: 2258.282 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 2291.461 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (141 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 77 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 8 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.014 0.007 198.7 85: (ns/day) (hour/ns) 85: Performance: 210.536 0.114 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.7 85: (ns/day) (hour/ns) 85: Performance: 1980.262 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 2292.314 0.010 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2117.770 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 2091.527 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 32 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1999.868 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (890 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.440 0.736 195.7 85: (ns/day) (hour/ns) 85: Performance: 1.996 12.025 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 59 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.252 0.658 190.3 85: (ns/day) (hour/ns) 85: Performance: 2.232 10.751 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2163.510 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2090.463 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1948.630 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 2101.516 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3464 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1730.504 0.014 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 2003.771 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2182.286 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 56 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.392 0.714 195.0 85: (ns/day) (hour/ns) 85: Performance: 2.057 11.666 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 2058.334 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 2046.029 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (2128 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1119.701 0.021 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1307.704 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.0%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1453.999 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1400.453 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1370.391 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.3%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1384.870 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (194 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1112.322 0.022 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1237.315 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.1%. 85: The balanceable part of the MD step is 69%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.072 1.052 197.0 85: (ns/day) (hour/ns) 85: Performance: 1.396 17.188 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1304.243 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.0%. 85: The balanceable part of the MD step is 64%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.761 0.881 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.668 14.389 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1301.351 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3073 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 60%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 191.3 85: (ns/day) (hour/ns) 85: Performance: 1089.888 0.022 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 1%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.0%. 85: 85: 85: NOTE: 10 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.662 0.331 200.0 85: (ns/day) (hour/ns) 85: Performance: 4.437 5.409 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.1%. 85: The balanceable part of the MD step is 68%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 52 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.124 1.078 197.0 85: (ns/day) (hour/ns) 85: Performance: 1.363 17.613 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.7%. 85: The balanceable part of the MD step is 62%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.532 0.766 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.918 12.516 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.1 85: (ns/day) (hour/ns) 85: Performance: 1174.229 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.3 85: (ns/day) (hour/ns) 85: Performance: 1208.433 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (4298 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.335 0.168 199.9 85: (ns/day) (hour/ns) 85: Performance: 8.759 2.740 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 57 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.099 1.050 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.399 17.149 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.2 85: (ns/day) (hour/ns) 85: Performance: 1498.381 0.016 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 199.2 85: (ns/day) (hour/ns) 85: Performance: 86.210 0.278 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1442.762 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.117 0.058 199.8 85: (ns/day) (hour/ns) 85: Performance: 25.111 0.956 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (2924 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 1136.746 0.021 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1286.136 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.3 85: (ns/day) (hour/ns) 85: Performance: 1404.924 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1355.019 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1344.667 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.563 0.281 199.9 85: (ns/day) (hour/ns) 85: Performance: 5.219 4.598 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (883 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1206.895 0.020 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.036 1.034 196.9 85: (ns/day) (hour/ns) 85: Performance: 1.421 16.893 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1438.047 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1331.157 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1328.860 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1330.294 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1685 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1045.586 0.023 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.992 1.012 196.9 85: (ns/day) (hour/ns) 85: Performance: 1.452 16.534 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1242.180 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1186.555 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1161.281 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1157.136 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1800 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.9 85: (ns/day) (hour/ns) 85: Performance: 827.981 0.029 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 189.9 85: (ns/day) (hour/ns) 85: Performance: 927.311 0.026 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.0 85: (ns/day) (hour/ns) 85: Performance: 975.086 0.025 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.8 85: (ns/day) (hour/ns) 85: Performance: 930.674 0.026 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 191.1 85: (ns/day) (hour/ns) 85: Performance: 957.953 0.025 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.483 0.242 199.9 85: (ns/day) (hour/ns) 85: Performance: 6.081 3.947 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1219 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 981.064 0.024 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1090.081 0.022 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1152.482 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1145.305 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1138.952 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1159.750 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (473 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (40069 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (40082 ms total) 85: [ PASSED ] 25 tests. 85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 40.11 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1704.647 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 2029.850 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 1961.973 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2215.244 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 1669.538 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2416.867 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1269 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1817.821 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 1977.719 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1267.873 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.4 86: (ns/day) (hour/ns) 86: Performance: 2232.099 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2268.260 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2253.326 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (976 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1631.513 0.015 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 2048.070 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2260.768 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2254.976 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2269.931 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2137.611 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1284 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 98.0 86: (ns/day) (hour/ns) 86: Performance: 769.401 0.031 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 2168.460 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2497.201 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2396.186 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2400.855 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2375.856 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (942 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 1846.147 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 2086.215 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2449.540 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2338.874 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2260.768 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2296.159 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1190 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1433.363 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2133.170 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2321.249 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2180.741 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2132.431 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2222.436 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1167 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1826.443 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1661.881 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2378.608 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2234.528 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1840.632 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2279.169 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (996 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1750.666 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1639.328 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 79.4 86: (ns/day) (hour/ns) 86: Performance: 1837.338 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2152.548 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2251.679 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2139.838 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1044 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1470.660 0.016 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1543.235 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2319.501 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2190.044 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2182.286 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2162.371 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1124 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.8 86: (ns/day) (hour/ns) 86: Performance: 1497.835 0.016 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.4 86: (ns/day) (hour/ns) 86: Performance: 279.811 0.086 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.6 86: (ns/day) (hour/ns) 86: Performance: 1483.408 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1710.326 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1708.429 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1536.691 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1582 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.7 86: (ns/day) (hour/ns) 86: Performance: 1375.133 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1463.324 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1710.326 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.6 86: (ns/day) (hour/ns) 86: Performance: 1612.299 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1293.427 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.8 86: (ns/day) (hour/ns) 86: Performance: 1355.764 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1215 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 1460.549 0.016 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1605.157 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1775.387 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1713.656 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1634.977 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1634.977 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (954 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.8 86: (ns/day) (hour/ns) 86: Performance: 1398.546 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1319.185 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.2 86: (ns/day) (hour/ns) 86: Performance: 289.040 0.083 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1622.063 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1630.649 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1631.081 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (932 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (14681 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (14696 ms total) 86: [ PASSED ] 13 tests. 86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 14.72 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 24 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 192.4 87: (ns/day) (hour/ns) 87: Performance: 1479.134 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1791.391 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.5%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 6 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 2001.818 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 28%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 18 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 15 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.636 0.840 194.8 87: (ns/day) (hour/ns) 87: Performance: 1.749 13.725 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.5%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1836.790 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 35%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1865.716 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3561 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.0 87: (ns/day) (hour/ns) 87: Performance: 1432.530 0.017 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1705.591 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 2033.870 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1786.974 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1752.409 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1802.397 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1453 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1457.439 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.0 87: (ns/day) (hour/ns) 87: Performance: 1680.238 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1808.747 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1814.875 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1821.583 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1706.063 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1158 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1520.946 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.7 87: (ns/day) (hour/ns) 87: Performance: 1834.329 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 2015.571 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1953.883 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1948.014 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 15 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.524 0.778 195.9 87: (ns/day) (hour/ns) 87: Performance: 1.888 12.712 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3402 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1473.650 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1780.518 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1980.898 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1812.739 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1838.434 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1883.398 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2069 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1481.090 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1796.091 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1987.930 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1488.246 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1874.230 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1813.006 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2144 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 192.5 87: (ns/day) (hour/ns) 87: Performance: 1483.765 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.4 87: (ns/day) (hour/ns) 87: Performance: 1746.695 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1938.513 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1746.943 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.4 87: (ns/day) (hour/ns) 87: Performance: 1825.902 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1871.383 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2077 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 22 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.150 0.575 200.0 87: (ns/day) (hour/ns) 87: Performance: 2.555 9.392 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1572.784 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.8 87: (ns/day) (hour/ns) 87: Performance: 1850.862 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1704.647 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1758.913 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.894 0.947 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.551 15.472 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4814 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.861 1.430 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.027 23.371 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.0 87: (ns/day) (hour/ns) 87: Performance: 1682.992 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1833.783 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.872 0.952 196.6 87: (ns/day) (hour/ns) 87: Performance: 1.543 15.555 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.4 87: (ns/day) (hour/ns) 87: Performance: 1831.058 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.1 87: (ns/day) (hour/ns) 87: Performance: 1555.509 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (4838 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 59%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1042.843 0.023 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1140.956 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.3 87: (ns/day) (hour/ns) 87: Performance: 1239.930 0.019 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1240.180 0.019 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.7 87: (ns/day) (hour/ns) 87: Performance: 1256.367 0.019 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1178.159 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1609 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 58%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 191.1 87: (ns/day) (hour/ns) 87: Performance: 941.052 0.026 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 55%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1087.483 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1226.843 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.8 87: (ns/day) (hour/ns) 87: Performance: 1194.145 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1152.698 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.7 87: (ns/day) (hour/ns) 87: Performance: 1153.345 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1529 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1023.695 0.023 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.2 87: (ns/day) (hour/ns) 87: Performance: 1179.174 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1020.304 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1238.684 0.019 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.3 87: (ns/day) (hour/ns) 87: Performance: 1208.789 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.1 87: (ns/day) (hour/ns) 87: Performance: 1207.960 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1667 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1018.448 0.024 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1150.760 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1212.000 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.477 0.739 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.988 12.071 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1096.484 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1113.528 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3565 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (33890 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (33901 ms total) 87: [ PASSED ] 13 tests. 87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 33.92 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.288 0.144 199.9 88: (ns/day) (hour/ns) 88: Performance: 10.199 2.353 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: NOTE: 10 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.130 0.065 199.7 88: (ns/day) (hour/ns) 88: Performance: 11.987 2.002 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (284 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: NOTE: 17 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.041 0.021 199.6 88: (ns/day) (hour/ns) 88: Performance: 8.339 2.878 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (37 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (322 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 694026239 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.829 0.915 200.0 88: (ns/day) (hour/ns) 88: Performance: 1.984 12.099 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (32903 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1153441793 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 2.094 1.047 200.0 88: (ns/day) (hour/ns) 88: Performance: 1.733 13.849 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (1340 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -272662531 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.637 0.818 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.217 10.826 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (1127 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -1208644673 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.679 0.339 200.0 88: (ns/day) (hour/ns) 88: Performance: 5.346 4.489 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (22198 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to 1073067867 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.678 0.339 200.0 88: (ns/day) (hour/ns) 88: Performance: 5.355 4.482 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (374 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to 872396797 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 3.946 1.973 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.423 5.427 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (2072 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 2008544511 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 2.569 1.285 200.0 88: (ns/day) (hour/ns) 88: Performance: 1.412 16.992 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (1650 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 2012216799 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.443 0.721 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.515 9.543 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (992 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -107776001 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.89 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.769 0.385 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.715 5.090 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (520 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.852 0.426 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.259 5.635 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -292552801 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.90 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (586 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -543179301 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.873 0.436 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.157 5.773 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (594 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -675287313 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.90 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.579 0.289 200.0 88: (ns/day) (hour/ns) 88: Performance: 6.270 3.828 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (367 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (64729 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (65066 ms total) 88: [ PASSED ] 14 tests. 88/92 Test #88: MdrunFEPTests ............................. Passed 65.08 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 11 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.186 0.093 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.502 1.231 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (273 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 10 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.184 0.092 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.694 1.219 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (250 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 10 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.187 0.094 199.9 89: (ns/day) (hour/ns) 89: Performance: 19.379 1.238 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (255 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 10 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.184 0.092 199.8 89: (ns/day) (hour/ns) 89: Performance: 19.686 1.219 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (249 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (1028 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (1044 ms total) 89: [ PASSED ] 4 tests. 89/92 Test #89: MdrunPullTests ............................ Passed 1.07 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -540693825 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.187 0.094 199.9 90: (ns/day) (hour/ns) 90: Performance: 48.028 0.500 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (108 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1535066110 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.188 0.094 199.9 90: (ns/day) (hour/ns) 90: Performance: 47.740 0.503 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (102 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1834989390 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.186 0.093 199.9 90: (ns/day) (hour/ns) 90: Performance: 48.254 0.497 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (102 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1007878470 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.188 0.094 199.9 90: (ns/day) (hour/ns) 90: Performance: 47.821 0.502 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (103 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 529955818 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.192 0.096 199.5 90: (ns/day) (hour/ns) 90: Performance: 46.792 0.513 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (104 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -4121 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.191 0.096 199.9 90: (ns/day) (hour/ns) 90: Performance: 46.939 0.511 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (104 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -204999043 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 20 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.192 0.096 199.9 90: (ns/day) (hour/ns) 90: Performance: 46.668 0.514 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (105 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -696854019 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.189 0.095 199.9 90: (ns/day) (hour/ns) 90: Performance: 47.513 0.505 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (104 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -28193861 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.192 0.096 199.9 90: (ns/day) (hour/ns) 90: Performance: 46.822 0.513 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (104 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 2146434999 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.192 0.096 199.9 90: (ns/day) (hour/ns) 90: Performance: 46.700 0.514 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (105 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -227595265 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.190 0.095 199.9 90: (ns/day) (hour/ns) 90: Performance: 47.313 0.507 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (104 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -69238817 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.182 0.091 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.360 0.486 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (98 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (1250 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (1258 ms total) 90: [ PASSED ] 12 tests. 90/92 Test #90: MdrunRotationTests ........................ Passed 1.28 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 0 tests from 0 test suites. 91: [==========] 0 tests from 0 test suites ran. (0 ms total) 91: [ PASSED ] 0 tests. 91: 91: YOU HAVE 82 DISABLED TESTS 91: 91/92 Test #91: MdrunSimulatorComparison .................. Passed 0.01 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /build/reproducible-path/gromacs-2025.1/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 1.4%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.5%. 92: 92: 92: NOTE: 38 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.003 0.002 194.4 92: (ns/day) (hour/ns) 92: Performance: 477.909 0.050 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: trr version: GMX_trn_file (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (26 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 1.8%. 92: The balanceable part of the MD step is 34%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.6%. 92: 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.5 92: (ns/day) (hour/ns) 92: Performance: 832.119 0.029 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (273 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 1.6%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.6%. 92: 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.6 92: (ns/day) (hour/ns) 92: Performance: 875.333 0.027 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (24 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 188.7 92: (ns/day) (hour/ns) 92: Performance: 1155.328 0.021 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (40 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 187.7 92: (ns/day) (hour/ns) 92: Performance: 1093.359 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (35 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 187.4 92: (ns/day) (hour/ns) 92: Performance: 1083.912 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (40 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 16 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 9 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.824 0.412 200.0 92: (ns/day) (hour/ns) 92: Performance: 1.887 12.722 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (905 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 187.8 92: (ns/day) (hour/ns) 92: Performance: 1075.158 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (26 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 188.3 92: (ns/day) (hour/ns) 92: Performance: 1045.182 0.023 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (43 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 1.7%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.6%. 92: 92: 92: NOTE: 27 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.7 92: (ns/day) (hour/ns) 92: Performance: 988.181 0.024 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (27 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 0.8%. 92: The balanceable part of the MD step is 41%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.3%. 92: 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.3 92: (ns/day) (hour/ns) 92: Performance: 975.472 0.025 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (28 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.0 92: (ns/day) (hour/ns) 92: Performance: 1070.745 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (33 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 188.3 92: (ns/day) (hour/ns) 92: Performance: 1023.213 0.023 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (51 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.6 92: (ns/day) (hour/ns) 92: Performance: 1003.227 0.024 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (31 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 27 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 188.3 92: (ns/day) (hour/ns) 92: Performance: 982.969 0.024 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (356 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.5 92: (ns/day) (hour/ns) 92: Performance: 1088.797 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (23 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.1 92: (ns/day) (hour/ns) 92: Performance: 1047.700 0.023 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (20 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.848 0.440 192.7 92: (ns/day) (hour/ns) 92: Performance: 1.767 13.580 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (977 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 190.1 92: (ns/day) (hour/ns) 92: Performance: 1069.341 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (51 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.848 0.440 192.8 92: (ns/day) (hour/ns) 92: Performance: 1.767 13.579 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (1259 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.001 0.001 189.0 92: (ns/day) (hour/ns) 92: Performance: 1080.143 0.022 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (255 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (4535 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (4554 ms total) 92: [ PASSED ] 37 tests. 92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 4.58 sec 100% tests passed, 0 tests failed out of 92 Label Time Summary: GTest = 1698.20 sec*proc (90 tests) IntegrationTest = 1486.84 sec*proc (29 tests) MpiTest = 1271.14 sec*proc (21 tests) QuickGpuTest = 151.43 sec*proc (23 tests) SlowGpuTest = 1503.49 sec*proc (14 tests) SlowTest = 198.69 sec*proc (14 tests) UnitTest = 12.67 sec*proc (47 tests) Total Test time (real) = 673.09 sec /usr/bin/make -j12 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && 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src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' 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/build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P 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make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build [ 0%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target scanner /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends 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cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 9%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 61%] Built target gmxapi make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 62%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/calcvir.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make 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make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 63%] Built target plumed_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target awh-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/freeenergyparameters.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/bonded.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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/build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target plumed_md-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp 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../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 64%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/arrayrefwithpadding.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 66%] Built target domdec-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 66%] Built target fft-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 67%] Built target nbnxm-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/bitmask128.cpp /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/position_restraints.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 67%] Built target listed_forces-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 67%] Built target mdspan-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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"CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 70%] Built target mdlib-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/normaldistribution.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pme.cpp [ 71%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 71%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 71%] Built target taskassignment-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 72%] Built target ewald-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 74%] Built target mdtypes-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 74%] Built target pbcutil-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" 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/build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 75%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 76%] Built target topology-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" [ 77%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build [ 77%] Built target pdb2gmx1-test make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" 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-DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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"CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 79%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target correlations-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ [ 80%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 80%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 81%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser 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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 83%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/requirements.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/mimic.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 84%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests 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"CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends 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CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/testmodule.cpp cd 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/boxdeformation.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 85%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 87%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 87%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 88%] Built target gmxpreprocess-test /usr/bin/make -f 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 89%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong 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../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp 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mdrun-non-integrator-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 90%] Built target selection-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests/traits.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 92%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests 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/usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/analysisdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 93%] Built target mdrun-fep-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd 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-I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 96%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/conversions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include 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-DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 97%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.1/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1384120321 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.008 0.004 196.7 1: (ns/day) (hour/ns) 1: Performance: 128.409 0.187 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (377 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -67108867 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 17 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.036 0.018 199.4 1: (ns/day) (hour/ns) 1: Performance: 28.285 0.849 1: [ OK ] GmxApiTest.RunnerBasicMD (388 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1212297221 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.172 0.086 199.9 1: (ns/day) (hour/ns) 1: Performance: 41.237 0.582 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.170 0.085 199.9 1: (ns/day) (hour/ns) 1: Performance: 41.562 0.577 1: [ OK ] GmxApiTest.RunnerReinitialize (465 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -253771777 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 17 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.036 0.018 199.2 1: (ns/day) (hour/ns) 1: Performance: 28.109 0.854 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 19 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.4 1: (ns/day) (hour/ns) 1: Performance: 31.312 0.766 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (333 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -20497 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 37 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.074 0.037 199.7 1: (ns/day) (hour/ns) 1: Performance: 22.670 1.059 1: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 31 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.3 1: (ns/day) (hour/ns) 1: Performance: 20.988 1.144 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (402 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -369238085 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (291 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (2260 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (2272 ms total) 1: [ PASSED ] 9 tests. 1/92 Test #1: GmxapiExternalInterfaceTests .............. Passed 2.32 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -604657189 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (322 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -537150566 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (279 ms) 2: [----------] 2 tests from GmxApiTest (601 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (621 ms total) 2: [ PASSED ] 2 tests. 2/92 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.64 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (15 ms) 3: [----------] 8 tests from NBlibTest (16 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (26 ms) 3: [----------] 1 test from LinearChainDataFixture (26 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (44 ms total) 3: [ PASSED ] 44 tests. 3/92 Test #3: NbLibListedForcesTests .................... Passed 0.06 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/92 Test #4: NbLibSamplesTestArgon ..................... Passed 0.02 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/92 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.07 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/92 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (1 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (1 ms total) 7: [ PASSED ] 57 tests. 7/92 Test #7: NbLibSetupTests ........................... Passed 0.03 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (41 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (5 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (15 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 8: [----------] 4 tests from TprReaderTest (77 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (85 ms total) 8: [ PASSED ] 4 tests. 8/92 Test #8: NbLibTprTests ............................. Passed 0.11 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (4 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (7 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (7 ms total) 9: [ PASSED ] 20 tests. 9/92 Test #9: NbLibIntegrationTests ..................... Passed 0.03 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/92 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (4 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (6 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (9 ms total) 11: [ PASSED ] 75 tests. 11/92 Test #11: TestUtilsUnitTests ........................ Passed 0.03 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (14 ms) 12: [----------] 1 test from MpiSelfTest (14 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (14 ms total) 12: [ PASSED ] 1 test. 12/92 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.03 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (0 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (0 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (0 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (6 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/92 Test #13: UtilityUnitTests .......................... Passed 0.04 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (18 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (19 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (38 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (38 ms total) 14: [ PASSED ] 2 tests. 14/92 Test #14: UtilityMpiUnitTests ....................... Passed 0.06 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (5 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (8 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (8 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (14 ms total) 15: [ PASSED ] 78 tests. 15/92 Test #15: GmxlibTests ............................... Passed 0.04 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (0 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (0 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (0 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (9 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (18 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (13 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (11 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (3 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (4 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (4 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (4 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (78 ms total) 16: [ PASSED ] 1032 tests. 16/92 Test #16: MdlibUnitTest ............................. Passed 0.18 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (0 ms) 17: [----------] 1 test from BiasTest (0 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (120 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (2556 ms) 17: [----------] 2 tests from BiasSharingTest (2677 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (14 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (11 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (13 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (2712 ms total) 17: [ PASSED ] 27 tests. 17/92 Test #17: AwhTest ................................... Passed 2.73 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (0 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (1 ms total) 18: [ PASSED ] 18 tests. 18/92 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.02 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -106196017 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -35131395 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (3 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -220468632 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to 1709178854 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (8 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -6297633 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (8 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 19: Setting the LD random seed to -1344545092 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (30 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (0 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (32 ms total) 19: [ PASSED ] 21 tests. 19/92 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.05 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -17645853 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (6 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (6 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -966841 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -566494465 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -9367561 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -269631826 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (13 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -549979393 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to 1854664567 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to -1879120529 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (35 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 20: Setting the LD random seed to 2079579643 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (40 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (82 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (103 ms total) 20: [ PASSED ] 16 tests. 20/92 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.13 sec test 21 Start 21: PlumedAppliedForcesUnitTests 21: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 21: Test timeout computed to be: 30 21: [==========] Running 8 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 8 tests from PlumedOptionsTest 21: [ RUN ] PlumedOptionsTest.defaultConstructor 21: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 21: [ RUN ] PlumedOptionsTest.setTimeStep 21: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 21: [ RUN ] PlumedOptionsTest.setStartingBehavior 21: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFile 21: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 21: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 21: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 21: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 21: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 21: [ RUN ] PlumedOptionsTest.setTopology 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: 21: NOTE 2 [file angles1.top, line 72]: 21: In moleculetype 'butane' 4 atoms are not bound by a potential or 21: constraint to any other atom in the same moleculetype. Although 21: technically this might not cause issues in a simulation, this often means 21: that the user forgot to add a bond/potential/constraint or put multiple 21: molecules in the same moleculetype definition by mistake. Run with -v to 21: get information for each atom. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 21: NVE simulation: will use the initial temperature of 238.919 K for 21: determining the Verlet buffer size 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 17493.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 21: NVE simulation: will use the initial temperature of 67.983 K for 21: determining the Verlet buffer size 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: There were 2 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 9.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 18.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: NVE simulation: will use the initial temperature of 135.187 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 21: Setting the LD random seed to -1451784723 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -151080965 21: 21: Generated 3 of the 3 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'butane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to 1572779125 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Argon' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon5832.gro' 21: Analysing residue names: 21: There are: 5832 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -201900066 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonA' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonB' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonC' 21: 21: Excluding 1 bonded neighbours molecule type 'ArgonD' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to 1593701111 21: 21: Generated 1 of the 1 non-bonded parameter combinations 21: 21: Excluding 1 bonded neighbours molecule type 'Dipole' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 21: Analysing residue names: 21: There are: 2 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: Setting the LD random seed to -1076908944 21: 21: Generated 331705 of the 331705 non-bonded parameter combinations 21: 21: Generated 331705 of the 331705 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Excluding 3 bonded neighbours molecule type 'methane' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 21: Analysing residue names: 21: There are: 1 Water residues 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] PlumedOptionsTest.setTopology (418 ms) 21: [----------] 8 tests from PlumedOptionsTest (418 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 8 tests from 1 test suite ran. (418 ms total) 21: [ PASSED ] 8 tests. 21/92 Test #21: PlumedAppliedForcesUnitTests .............. Passed 0.45 sec test 22 Start 22: PlumedMDTests 22: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/plumed/tests 22: Test timeout computed to be: 600 22: [==========] Running 2 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from SimplePlumedMD/PlumedRun 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 22: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 22: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 22: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test suite ran. (7 ms total) 22: [ PASSED ] 0 tests. 22: [ SKIPPED ] 2 tests, listed below: 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 22: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 22/92 Test #22: PlumedMDTests ............................. Passed 0.03 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from NNPotTest (0 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (0 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to 1428086493 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to 2012741365 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -754757 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (10 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 23: Setting the LD random seed to -144704929 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (8 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (24 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (25 ms total) 23: [ PASSED ] 12 tests. 23/92 Test #23: NNPotAppliedForcesUnitTest ................ Passed 0.05 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (0 ms total) 24: [ PASSED ] 3 tests. 24/92 Test #24: AppliedForcesUnitTest ..................... Passed 0.01 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (3 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (1 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (2 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (11 ms total) 25: [ PASSED ] 132 tests. 25/92 Test #25: ListedForcesTest .......................... Passed 0.03 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 383 tests from 4 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (0 ms total) 26: 26: [----------] 2 tests from SimdEnergyAccumulatorTest 26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 26: 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (9 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (384 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 383 tests from 4 test suites ran. (385 ms total) 26: [ PASSED ] 185 tests. 26: [ SKIPPED ] 198 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/92 Test #26: NbnxmTests ................................ Passed 0.42 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/92 Test #27: NbnxmGpuTests ............................. Passed 0.02 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (4 ms total) 28: [ PASSED ] 60 tests. 28/92 Test #28: CommandLineUnitTests ...................... Passed 0.02 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/92 Test #29: DomDecTests ............................... Passed 0.03 sec test 30 Start 30: DomDecMpiTests 30: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (25 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (15 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (27 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (28 ms) 30: [----------] 4 tests from HaloExchangeTest (97 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (97 ms total) 30: [ PASSED ] 4 tests. 30/92 Test #30: DomDecMpiTests ............................ Passed 0.13 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (79 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from Pme_SolveTest (8 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (4 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (7 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [----------] 72 tests from Pme_GatherTest (9 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (2 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (33 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (148 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/92 Test #31: EwaldUnitTests ............................ Passed 0.18 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (1 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (4 ms) 32: [----------] 2 tests from ManyFFTTest (6 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (0 ms) 32: [----------] 1 test from FFTTest (1 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (6 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (15 ms total) 32: [ PASSED ] 15 tests. 32/92 Test #32: FFTUnitTests .............................. Passed 0.04 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (0 ms total) 33: [ PASSED ] 67 tests. 33/92 Test #33: GpuUtilsUnitTests ......................... Passed 0.03 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (0 ms) 34: [----------] 1 test from CpuInfoTest (0 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (7 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (7 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (7 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (7 ms) 34: [----------] 4 tests from HardwareTopologyTest (28 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (0 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (39 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/92 Test #34: HardwareUnitTests ......................... Passed 0.06 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (0 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (23 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (23 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (48 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 35: [----------] 2 tests from NelderMead (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (4 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (65 ms total) 35: [ PASSED ] 328 tests. 35/92 Test #35: MathUnitTests ............................. Passed 0.10 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 36: [----------] 17 tests from ThreadAffinityTest (3 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (3 ms total) 36: [ PASSED ] 21 tests. 36/92 Test #36: MdrunUtilityUnitTests ..................... Passed 0.03 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (53 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (120 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (59 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (56 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (59 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (71 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (421 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (91 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (163 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (67 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (168 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (48 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (46 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (67 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (655 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (1077 ms total) 37: [ PASSED ] 13 tests. 37/92 Test #37: MdrunUtilityMpiUnitTests .................. Passed 1.10 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (0 ms total) 38: [ PASSED ] 32 tests. 38/92 Test #38: MDSpanTests ............................... Passed 0.02 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 39: [----------] 2 tests from CheckpointDataTest (3 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (0 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (4 ms total) 39: [ PASSED ] 97 tests. 39/92 Test #39: MdtypesUnitTest ........................... Passed 0.03 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (0 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 40: [----------] 3 tests from HelpManagerTest (0 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 40: [----------] 11 tests from HelpWriterContextTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (1 ms total) 40: [ PASSED ] 22 tests. 40/92 Test #40: OnlineHelpUnitTests ....................... Passed 0.03 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (0 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (0 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (3 ms total) 41: [ PASSED ] 112 tests. 41/92 Test #41: OptionsUnitTests .......................... Passed 0.02 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 37 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (0 ms total) 42: 42: [----------] 5 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 42: [----------] 5 tests from PbcTest (0 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 37 tests from 5 test suites ran. (3 ms total) 42: [ PASSED ] 37 tests. 42/92 Test #42: PbcutilUnitTest ........................... Passed 0.02 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (0 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (0 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (0 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (1 ms total) 43: [ PASSED ] 44 tests. 43/92 Test #43: RandomUnitTests ........................... Passed 0.01 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (0 ms total) 44: [ PASSED ] 1 test. 44/92 Test #44: RestraintTests ............................ Passed 0.02 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 20 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (0 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (6 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (10 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (11 ms) 45: [ RUN ] SplineTableTest/0.Simd 45: [ OK ] SplineTableTest/0.Simd (2 ms) 45: [ RUN ] SplineTableTest/0.SimdTwoFunctions 45: [ OK ] SplineTableTest/0.SimdTwoFunctions (12 ms) 45: [----------] 10 tests from SplineTableTest/0 (44 ms total) 45: 45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (0 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (13 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (25 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (28 ms) 45: [ RUN ] SplineTableTest/1.Simd 45: [ OK ] SplineTableTest/1.Simd (5 ms) 45: [ RUN ] SplineTableTest/1.SimdTwoFunctions 45: [ OK ] SplineTableTest/1.SimdTwoFunctions (38 ms) 45: [----------] 10 tests from SplineTableTest/1 (114 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 20 tests from 2 test suites ran. (158 ms total) 45: [ PASSED ] 20 tests. 45/92 Test #45: TableUnitTests ............................ Passed 0.17 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (0 ms total) 46: [ PASSED ] 3 tests. 46/92 Test #46: TaskAssignmentUnitTests ................... Passed 0.02 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (2 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (2 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (2 ms total) 47: [ PASSED ] 6 tests. 47/92 Test #47: GmxTimingTests ............................ Passed 0.02 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (1 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (5 ms) 48: [----------] 3 tests from IndexTest (9 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (1 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (0 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (5 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (16 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/92 Test #48: TopologyTest .............................. Passed 0.04 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (0 ms total) 49: [ PASSED ] 10 tests. 49/92 Test #49: PullTest .................................. Passed 0.01 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 247 tests from 19 test suites. 50: [----------] Global test environment set-up. 50: [----------] 6 tests from SimdBootstrapTest 50: [ RUN ] SimdBootstrapTest.loadStore 50: [ OK ] SimdBootstrapTest.loadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.loadU 50: [ OK ] SimdBootstrapTest.loadU (0 ms) 50: [ RUN ] SimdBootstrapTest.storeU 50: [ OK ] SimdBootstrapTest.storeU (0 ms) 50: [ RUN ] SimdBootstrapTest.loadStoreI 50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 50: [ RUN ] SimdBootstrapTest.loadUI 50: [ OK ] SimdBootstrapTest.loadUI (0 ms) 50: [ RUN ] SimdBootstrapTest.storeUI 50: [ OK ] SimdBootstrapTest.storeUI (0 ms) 50: [----------] 6 tests from SimdBootstrapTest (0 ms total) 50: 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (0 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (0 ms total) 50: 50: [----------] 1 test from SimdTest 50: [ RUN ] SimdTest.GmxAligned 50: [ OK ] SimdTest.GmxAligned (0 ms) 50: [----------] 1 test from SimdTest (0 ms total) 50: 50: [----------] 42 tests from SimdFloatingpointTest 50: [ RUN ] SimdFloatingpointTest.setZero 50: [ OK ] SimdFloatingpointTest.setZero (0 ms) 50: [ RUN ] SimdFloatingpointTest.set 50: [ OK ] SimdFloatingpointTest.set (0 ms) 50: [ RUN ] SimdFloatingpointTest.add 50: [ OK ] SimdFloatingpointTest.add (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskAdd 50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 50: [ RUN ] SimdFloatingpointTest.sub 50: [ OK ] SimdFloatingpointTest.sub (0 ms) 50: [ RUN ] SimdFloatingpointTest.mul 50: [ OK ] SimdFloatingpointTest.mul (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzMul 50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 50: [ RUN ] SimdFloatingpointTest.fma 50: [ OK ] SimdFloatingpointTest.fma (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzFma 50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fms 50: [ OK ] SimdFloatingpointTest.fms (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnma 50: [ OK ] SimdFloatingpointTest.fnma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnms 50: [ OK ] SimdFloatingpointTest.fnms (0 ms) 50: [ RUN ] SimdFloatingpointTest.abs 50: [ OK ] SimdFloatingpointTest.abs (0 ms) 50: [ RUN ] SimdFloatingpointTest.neg 50: [ OK ] SimdFloatingpointTest.neg (0 ms) 50: [ RUN ] SimdFloatingpointTest.and 50: [ OK ] SimdFloatingpointTest.and (0 ms) 50: [ RUN ] SimdFloatingpointTest.or 50: [ OK ] SimdFloatingpointTest.or (0 ms) 50: [ RUN ] SimdFloatingpointTest.xor 50: [ OK ] SimdFloatingpointTest.xor (0 ms) 50: [ RUN ] SimdFloatingpointTest.andNot 50: [ OK ] SimdFloatingpointTest.andNot (0 ms) 50: [ RUN ] SimdFloatingpointTest.max 50: [ OK ] SimdFloatingpointTest.max (0 ms) 50: [ RUN ] SimdFloatingpointTest.min 50: [ OK ] SimdFloatingpointTest.min (0 ms) 50: [ RUN ] SimdFloatingpointTest.round 50: [ OK ] SimdFloatingpointTest.round (0 ms) 50: [ RUN ] SimdFloatingpointTest.roundMode 50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 50: [ RUN ] SimdFloatingpointTest.trunc 50: [ OK ] SimdFloatingpointTest.trunc (0 ms) 50: [ RUN ] SimdFloatingpointTest.frexp 50: [ OK ] SimdFloatingpointTest.frexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.ldexp 50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.rsqrt 50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRsqrt 50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.rcp 50: [ OK ] SimdFloatingpointTest.rcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRcp 50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.selectByNotMask 50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpNe 50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLe 50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLt 50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 50: [ RUN ] SimdFloatingpointTest.testBits 50: [ OK ] SimdFloatingpointTest.testBits (0 ms) 50: [ RUN ] SimdFloatingpointTest.andB 50: [ OK ] SimdFloatingpointTest.andB (0 ms) 50: [ RUN ] SimdFloatingpointTest.orB 50: [ OK ] SimdFloatingpointTest.orB (0 ms) 50: [ RUN ] SimdFloatingpointTest.anyTrueB 50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 50: [ RUN ] SimdFloatingpointTest.blend 50: [ OK ] SimdFloatingpointTest.blend (0 ms) 50: [ RUN ] SimdFloatingpointTest.reduce 50: [ OK ] SimdFloatingpointTest.reduce (1 ms) 50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 50: [----------] 42 tests from SimdFloatingpointTest (1 ms total) 50: 50: [----------] 13 tests from SimdFloatingpointUtilTest 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 50: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 50: 50: [----------] 23 tests from SimdIntegerTest 50: [ RUN ] SimdIntegerTest.setZero 50: [ OK ] SimdIntegerTest.setZero (0 ms) 50: [ RUN ] SimdIntegerTest.set 50: [ OK ] SimdIntegerTest.set (0 ms) 50: [ RUN ] SimdIntegerTest.add 50: [ OK ] SimdIntegerTest.add (0 ms) 50: [ RUN ] SimdIntegerTest.sub 50: [ OK ] SimdIntegerTest.sub (0 ms) 50: [ RUN ] SimdIntegerTest.mul 50: [ OK ] SimdIntegerTest.mul (0 ms) 50: [ RUN ] SimdIntegerTest.and 50: [ OK ] SimdIntegerTest.and (0 ms) 50: [ RUN ] SimdIntegerTest.andNot 50: [ OK ] SimdIntegerTest.andNot (0 ms) 50: [ RUN ] SimdIntegerTest.or 50: [ OK ] SimdIntegerTest.or (0 ms) 50: [ RUN ] SimdIntegerTest.xor 50: [ OK ] SimdIntegerTest.xor (0 ms) 50: [ RUN ] SimdIntegerTest.extract 50: [ OK ] SimdIntegerTest.extract (0 ms) 50: [ RUN ] SimdIntegerTest.cvtR2I 50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvttR2I 50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvtI2R 50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpLt 50: [ OK ] SimdIntegerTest.cmpLt (0 ms) 50: [ RUN ] SimdIntegerTest.testBits 50: [ OK ] SimdIntegerTest.testBits (0 ms) 50: [ RUN ] SimdIntegerTest.andB 50: [ OK ] SimdIntegerTest.andB (0 ms) 50: [ RUN ] SimdIntegerTest.orB 50: [ OK ] SimdIntegerTest.orB (0 ms) 50: [ RUN ] SimdIntegerTest.anyTrue 50: [ OK ] SimdIntegerTest.anyTrue (0 ms) 50: [ RUN ] SimdIntegerTest.blend 50: [ OK ] SimdIntegerTest.blend (0 ms) 50: [ RUN ] SimdIntegerTest.cvtB2IB 50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 50: [ RUN ] SimdIntegerTest.cvtIB2B 50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 50: [----------] 23 tests from SimdIntegerTest (0 ms total) 50: 50: [----------] 56 tests from SimdMathTest 50: [ RUN ] SimdMathTest.generateTestPointsDouble 50: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) 50: [ RUN ] SimdMathTest.copysign 50: [ OK ] SimdMathTest.copysign (0 ms) 50: [ RUN ] SimdMathTest.invsqrt 50: [ OK ] SimdMathTest.invsqrt (0 ms) 50: [ RUN ] SimdMathTest.maskzInvsqrt 50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPair 50: [ OK ] SimdMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdMathTest.sqrt 50: [ OK ] SimdMathTest.sqrt (0 ms) 50: [ RUN ] SimdMathTest.sqrtUnsafe 50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 50: [ RUN ] SimdMathTest.inv 50: [ OK ] SimdMathTest.inv (0 ms) 50: [ RUN ] SimdMathTest.maskzInv 50: [ OK ] SimdMathTest.maskzInv (0 ms) 50: [ RUN ] SimdMathTest.cbrt 50: [ OK ] SimdMathTest.cbrt (0 ms) 50: [ RUN ] SimdMathTest.invcbrt 50: [ OK ] SimdMathTest.invcbrt (0 ms) 50: [ RUN ] SimdMathTest.log2 50: [ OK ] SimdMathTest.log2 (0 ms) 50: [ RUN ] SimdMathTest.log 50: [ OK ] SimdMathTest.log (0 ms) 50: [ RUN ] SimdMathTest.exp2 50: [ OK ] SimdMathTest.exp2 (0 ms) 50: [ RUN ] SimdMathTest.exp2Unsafe 50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 50: [ RUN ] SimdMathTest.exp 50: [ OK ] SimdMathTest.exp (0 ms) 50: [ RUN ] SimdMathTest.expUnsafe 50: [ OK ] SimdMathTest.expUnsafe (0 ms) 50: [ RUN ] SimdMathTest.pow 50: [ OK ] SimdMathTest.pow (0 ms) 50: [ RUN ] SimdMathTest.powUnsafe 50: [ OK ] SimdMathTest.powUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erf 50: [ OK ] SimdMathTest.erf (0 ms) 50: [ RUN ] SimdMathTest.erfc 50: [ OK ] SimdMathTest.erfc (0 ms) 50: [ RUN ] SimdMathTest.sin 50: [ OK ] SimdMathTest.sin (0 ms) 50: [ RUN ] SimdMathTest.cos 50: [ OK ] SimdMathTest.cos (0 ms) 50: [ RUN ] SimdMathTest.tan 50: [ OK ] SimdMathTest.tan (1 ms) 50: [ RUN ] SimdMathTest.asin 50: [ OK ] SimdMathTest.asin (0 ms) 50: [ RUN ] SimdMathTest.acos 50: [ OK ] SimdMathTest.acos (0 ms) 50: [ RUN ] SimdMathTest.atan 50: [ OK ] SimdMathTest.atan (0 ms) 50: [ RUN ] SimdMathTest.atan2 50: [ OK ] SimdMathTest.atan2 (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrection 50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrection 50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracy 50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.invSingleAccuracy 50: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cbrtSingleAccuracy 50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.log2SingleAccuracy 50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.logSingleAccuracy 50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracy 50: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracy 50: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracy 50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erfSingleAccuracy 50: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.erfcSingleAccuracy 50: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sinSingleAccuracy 50: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.cosSingleAccuracy 50: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.tanSingleAccuracy 50: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.asinSingleAccuracy 50: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.acosSingleAccuracy 50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atanSingleAccuracy 50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atan2SingleAccuracy 50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 56 tests from SimdMathTest (23 ms total) 50: 50: [----------] 1 test from EmptyArrayRefTest 50: [ RUN ] EmptyArrayRefTest.IsEmpty 50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 50: [----------] 1 test from EmptyArrayRefTest (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/0.Assignment 50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/1.Assignment 50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/0.Basic 50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/1.Basic 50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 50: 50: [----------] 3 tests from SimdVectorOperationsTest 50: [ RUN ] SimdVectorOperationsTest.iprod 50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 50: [ RUN ] SimdVectorOperationsTest.norm2 50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 50: [ RUN ] SimdVectorOperationsTest.cprod 50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 247 tests from 19 test suites ran. (26 ms total) 50: [ PASSED ] 247 tests. 50/92 Test #50: SimdUnitTests ............................. Passed 0.05 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (0 ms total) 51: [ PASSED ] 9 tests. 51/92 Test #51: CompatibilityHelpersTests ................. Passed 0.01 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (0 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (428 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (208 ms) 52: [----------] 2 tests from GmxChiTest (718 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (6 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (0 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (0 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (0 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (0 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (0 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (0 ms) 52: [----------] 10 tests from MindistTest (9 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (10 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (739 ms total) 52: [ PASSED ] 31 tests. 52/92 Test #52: GmxAnaTest ................................ Passed 0.76 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 215 tests from 15 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (1 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 53: [----------] 4 tests from GenconfTest (2 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to -1629634595 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (264 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to -1749681153 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (284 ms) 53: [----------] 2 tests from GenionTest (548 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (0 ms) 53: [----------] 1 test from GenRestrTest (0 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 53: Setting the LD random seed to 840679385 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -55574881 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to -41009 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -137541 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: Setting the LD random seed to -807995409 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -571216645 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (11 ms) 53: [----------] 3 tests from GromppDirectiveTest (17 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (0 ms) 53: [----------] 6 tests from InsertMoleculesTest (6 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (7 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (5 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (1 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (3 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (8 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (2 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (10 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [----------] 35 tests from GetIrTest (91 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (2 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (11 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (11 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (6 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (47 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 53: [----------] 6 tests from SolvateTest (84 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (0 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (8 ms total) 53: 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: Setting the LD random seed to -335873219 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (9 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: Setting the LD random seed to 2113746903 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 2046719927 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -353898642 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (3 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -1755908579 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1208771082 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 1070935657 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -607053969 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -269230346 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -272631317 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: Setting the LD random seed to 1992024455 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (8 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: Setting the LD random seed to -437264417 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 2004811262 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: Setting the LD random seed to -1887847717 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (9 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: Setting the LD random seed to -1633 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -848824449 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (13 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: Setting the LD random seed to -111434817 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -847257648 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (13 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: Setting the LD random seed to -537002625 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1813389577 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: Setting the LD random seed to -541735533 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -360515 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Setting the LD random seed to 1212578126 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 750059327 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Setting the LD random seed to -134611214 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1682080835 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (16 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: Setting the LD random seed to 2054880867 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -75531780 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (16 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to 2143190511 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1049122 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -142608642 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1734996731 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Setting the LD random seed to -281612358 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (11 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: Setting the LD random seed to 939519931 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1086370234 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 53: Setting the LD random seed to -543187241 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (15 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 114]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -822649218 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -68307125 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (2 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 53: Setting the LD random seed to -71630946 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (25 ms) 53: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (239 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 215 tests from 15 test suites ran. (1000 ms total) 53: [ PASSED ] 175 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/92 Test #53: GmxPreprocessTests ........................ Passed 1.02 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (73 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (48 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (53 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (813 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (813 ms total) 54: [ PASSED ] 30 tests. 54/92 Test #54: Pdb2gmx1Test .............................. Passed 0.83 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (29 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (22 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (510 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (43 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (44 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (536 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (1046 ms total) 55: [ PASSED ] 40 tests. 55/92 Test #55: Pdb2gmx2Test .............................. Passed 1.07 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (60 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (307 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (28 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (70 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (9 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (327 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (19 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (17 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (153 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (13 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (52 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.563 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (205 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (59 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.563 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (313 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (98 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (676 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (1526 ms total) 56: [ PASSED ] 39 tests. 56/92 Test #56: Pdb2gmx3Test .............................. Passed 1.54 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (59 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (27 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (41 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (47 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (0 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (58 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (51 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (116 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (1 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (57 ms) 57: [----------] 10 tests from AutocorrTest (464 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (9 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (1 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (1 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (3 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (7 ms) 57: [----------] 10 tests from ExpfitTest (27 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (493 ms total) 57: [ PASSED ] 21 tests. 57/92 Test #57: CorrelationsTest .......................... Passed 0.51 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 58: [----------] 6 tests from AverageModuleTest (1 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from BinAverageModuleTest (0 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from LifetimeModuleTest (0 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (13 ms total) 58: [ PASSED ] 69 tests. 58/92 Test #58: AnalysisDataUnitTests ..................... Passed 0.03 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (8 ms) 59: [----------] 1 test from OutputSelectorDeathTest (8 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (4 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (0 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 59: [----------] 5 tests from SetAtomsTest (4 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (5 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (2 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (6 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (11 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (10 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (56 ms total) 59: [ PASSED ] 67 tests. 59/92 Test #59: CoordinateIOTests ......................... Passed 0.08 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 60: [----------] 11 tests from AngleModuleTest (14 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (0 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (1 ms) 60: [----------] 5 tests from ClustsizeTest (4 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (2 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (5 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (13 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) 60: [----------] 6 tests from DistanceModuleTest (16 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (2 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (43 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (42 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (85 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -136610399 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (15 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to -46137365 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (15 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1418567681 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (12 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -1082589225 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (14 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -4408325 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (12 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 1270869626 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (14 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -16926801 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (14 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -579601671 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (14 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -8650778 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (15 ms) 60: [----------] 13 tests from MsdModuleTest (135 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 60: [----------] 9 tests from PairDistanceModuleTest (11 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (10 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (9 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (4 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (12 ms) 60: [----------] 5 tests from RdfModuleTest (47 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (5 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) 60: [----------] 5 tests from SasaModuleTest (20 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (2 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 60: [----------] 8 tests from SelectModuleTest (12 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 60: [----------] 10 tests from SurfaceAreaTest (5 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 60: Setting the LD random seed to 2146828031 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (295 ms) 60: [----------] 4 tests from TopologyInformation (297 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 60: [----------] 4 tests from TrajectoryModuleTest (5 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (18 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (10 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (11 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (13 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (9 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (12 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (2113 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (3 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (12 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (7 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (6 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (36 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (43 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (36 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (36 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (36 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (37 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (38 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (40 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (39 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (41 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (42 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (40 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (3102 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (7 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (169 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (38 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (223 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (6129 ms total) 60: [ PASSED ] 393 tests. 60/92 Test #60: TrajectoryAnalysisUnitTests ............... Passed 6.16 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (7 ms) 61: [----------] 1 test from DhdlTest (7 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (6 ms) 61: [----------] 1 test from OriresTest (6 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 61: [----------] 5 tests from EnergyTest (4 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (87 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (88 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (56 ms) 61: [----------] 3 tests from ViscosityTest (232 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (251 ms total) 61: [ PASSED ] 12 tests. 61/92 Test #61: EnergyAnalysisUnitTests ................... Passed 0.27 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -1074296859 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = -1074296859 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 57082 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 62: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 62: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 62: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 62: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 62: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 62: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 62: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 62: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 62: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 62: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 62: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 62: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 62: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 62: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 62: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 62: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 62: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 62: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 62: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 62: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 62: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 62: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 62: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 62: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 62: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 62: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 62: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 62: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 62: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 62: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 62: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 62: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 62: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 62: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 62: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 62: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 62: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 62: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 62: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 62: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 62: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 62: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 62: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 62: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 62: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 62: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 62: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 62: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 62: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 62: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 62: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 62: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 62: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 62: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 62: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 62: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 62: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 62: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 62: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 62: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 62: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 62: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 62: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 62: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 62: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 62: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 62: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 62: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 62: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 62: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 62: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 62: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 62: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 62: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 62: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 62: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 62: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 62: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 62: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 62: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 62: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 62: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 62: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 62: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 62: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 62: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 62: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 62: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 62: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 62: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 62: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 62: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 62: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 62: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 62: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 62: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 62: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 62: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 62: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 62: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 62: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 62: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 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0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (11 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 62: [----------] 2 tests from DumpTest (11 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 62: [----------] 3 tests from HelpwritingTest (0 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (2 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (0 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (1 ms) 62: [----------] 7 tests from GmxMakeNdx (6 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -272688257 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (4 ms) 62: [----------] 4 tests from ReportMethodsTest (4 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -20982145 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (269 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to 469731179 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (262 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to -271106441 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (381 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to 1575943803 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (268 ms) 62: [----------] 4 tests from ConvertTprTest (1182 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 62: Setting the LD random seed to 1065287679 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (270 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (270 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (4 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (9 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (2082 ms total) 62: [ PASSED ] 63 tests. 62/92 Test #62: ToolUnitTests ............................. Passed 2.10 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Setting the LD random seed to -60965121 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (327 ms) 63: [----------] 1 test from ConvertTprTest (327 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 63: Setting the LD random seed to -1617314890 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (256 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (256 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (584 ms total) 63: [ PASSED ] 2 tests. 63/92 Test #63: ToolWithLeaksUnitTests .................... Passed 0.61 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (0 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 64: [----------] 1 test from StructureIOTest (0 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (0 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (0 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (0 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 64: [----------] 4 tests from MatioTest (1 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (4 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 64: [----------] 4 tests from MrcDensityMap (5 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (0 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (11 ms total) 64: [ PASSED ] 421 tests. 64/92 Test #64: FileIOTests ............................... Passed 0.04 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (0 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 65: [----------] 11 tests from IndexMapTest (1 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (22 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (53 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 65: [----------] 13 tests from PositionCalculationTest (1 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 65: [----------] 33 tests from SelectionCollectionTest (6 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (2 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (29 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 65: [----------] 17 tests from SelectionOptionTest (2 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 65: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (100 ms total) 65: [ PASSED ] 201 tests. 65/92 Test #65: SelectionUnitTests ........................ Passed 0.13 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (8 ms) 66: [----------] 1 test from MdrunTest (8 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 1836973631 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.007 0.003 196.6 66: (ns/day) (hour/ns) 66: Performance: 50.815 0.472 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (10 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -134513797 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 25 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.023 0.011 199.2 66: (ns/day) (hour/ns) 66: Performance: 15.197 1.579 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (18 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -4219535 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 26 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.022 0.011 199.2 66: (ns/day) (hour/ns) 66: Performance: 15.320 1.567 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (18 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (48 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.122 0.061 199.8 66: (ns/day) (hour/ns) 66: Performance: 24.023 0.999 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (67 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 13 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.139 0.069 199.9 66: (ns/day) (hour/ns) 66: Performance: 21.166 1.134 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (75 ms) 66: [----------] 2 tests from Argon12/OutputFiles (143 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 855572446 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.068 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.663 1.359 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (43 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 1860893822 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.067 0.034 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.979 1.335 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (42 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -1050114 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.7 66: (ns/day) (hour/ns) 66: Performance: 18.329 1.309 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (42 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (128 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -612705 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.017 199.5 66: (ns/day) (hour/ns) 66: Performance: 14.873 1.614 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (26 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -88131993 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.5 66: (ns/day) (hour/ns) 66: Performance: 14.626 1.641 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (26 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1879114010 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 199.5 66: (ns/day) (hour/ns) 66: Performance: 15.036 1.596 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (26 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (79 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (436 ms total) 66: [ PASSED ] 12 tests. 66/92 Test #66: MdrunOutputTests .......................... Passed 0.45 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.85652608067156e+03 67: Maximum force = 4.50998690851897e+03 on atom 3 67: Norm of force = 1.68168494163492e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 435477951 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (16 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.82077921283928e+03 67: Maximum force = 7.39548334240075e+03 on atom 2 67: Norm of force = 2.78250777177324e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -704644126 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (24 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (10 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.47393359520241e+03 67: Maximum force = 6.13219949575544e+03 on atom 2 67: Norm of force = 1.77021426574818e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -455225421 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (56 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (8 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.85652608067156e+03 67: Maximum force = 4.50998690851897e+03 on atom 3 67: Norm of force = 1.68168494163492e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1870057439 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (23 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.71386626041483e+04 67: Maximum force = 6.78276506555709e+03 on atom 2 67: Norm of force = 1.96088641457984e+03 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -939541838 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (16 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: 67: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 67: Setting the LD random seed to -807035417 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (11 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 1610282813 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 19 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.030 0.015 199.4 67: (ns/day) (hour/ns) 67: Performance: 17.443 1.376 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 16 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.039 0.019 199.4 67: (ns/day) (hour/ns) 67: Performance: 22.330 1.075 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (44 ms) 67: [----------] 9 tests from DensityFittingTest (211 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 59 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.010 0.005 199.1 67: (ns/day) (hour/ns) 67: Performance: 17.624 1.362 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2112581595 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (10 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 62 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.010 0.005 199.0 67: (ns/day) (hour/ns) 67: Performance: 17.702 1.356 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2130575027 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (10 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 61 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.009 0.005 199.2 67: (ns/day) (hour/ns) 67: Performance: 18.299 1.312 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2109725678 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (9 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 52 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.011 0.006 199.3 67: (ns/day) (hour/ns) 67: Performance: 15.293 1.569 67: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1690038221 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (17 ms) 67: [----------] 4 tests from MimicTest (48 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 40261. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -1073873729 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 41 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.049 0.024 199.6 67: (ns/day) (hour/ns) 67: Performance: 21.296 1.127 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (113 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 47363. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.19770464690297e+03 67: Maximum force = 1.77948604657896e+04 on atom 9 67: Norm of force = 7.87328617833980e+03 67: Setting the LD random seed to -436240521 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (78 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (192 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (485 ms total) 67: [ PASSED ] 15 tests. 67/92 Test #67: MdrunModulesTests ......................... Passed 0.50 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to 1020524927 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1124098289 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (3 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -268567556 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: Setting the LD random seed to -34357379 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (4 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to -75763789 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to 460454598 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to 1702401887 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: Setting the LD random seed to -3670409 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (6 ms) 68: [----------] 9 tests from GromppTest (30 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -536875805 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.032 0.016 199.4 68: (ns/day) (hour/ns) 68: Performance: 16.279 1.474 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.013 199.4 68: (ns/day) (hour/ns) 68: Performance: 19.411 1.236 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (53 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 1, rlist from 1.035 to 1 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to -202392361 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: NOTE: 41 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 199.4 68: (ns/day) (hour/ns) 68: Performance: 12.334 1.946 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 102 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.477 0.239 200.0 68: (ns/day) (hour/ns) 68: Performance: 36.911 0.650 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (263 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1713443107 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 199.4 68: (ns/day) (hour/ns) 68: Performance: 12.167 1.972 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.5 68: (ns/day) (hour/ns) 68: Performance: 19.094 1.257 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 6 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.4 68: (ns/day) (hour/ns) 68: Performance: 18.916 1.269 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 8 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.4 68: (ns/day) (hour/ns) 68: Performance: 19.113 1.256 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 43 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.014 0.007 196.6 68: (ns/day) (hour/ns) 68: Performance: 12.492 1.921 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (123 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -1073959185 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 199.5 68: (ns/day) (hour/ns) 68: Performance: 17.271 1.390 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 199.6 68: (ns/day) (hour/ns) 68: Performance: 20.759 1.156 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (50 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 1740173295 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 199.4 68: (ns/day) (hour/ns) 68: Performance: 17.062 1.407 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (24 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -411712794 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 20 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.015 199.4 68: (ns/day) (hour/ns) 68: Performance: 16.804 1.428 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Setting nsteps to 4 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.013 199.5 68: (ns/day) (hour/ns) 68: Performance: 19.265 1.246 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (40 ms) 68: [----------] 6 tests from MdrunTerminationTest (556 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 21.522 1.115 68: trr version: GMX_trn_file (double precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (76 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.168 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.495 1.372 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (89 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (166 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.123 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.939 1.003 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.600 1.062 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.512 1.066 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (148 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 24.079 0.997 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.560 1.064 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.643 1.060 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (147 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.138 0.069 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.218 1.131 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.773 1.214 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.333 1.180 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (161 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.139 0.069 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.172 1.134 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.752 1.215 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.077 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.238 1.186 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (162 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.123 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.911 1.004 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.7 68: (ns/day) (hour/ns) 68: Performance: 21.652 1.108 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 199.6 68: (ns/day) (hour/ns) 68: Performance: 27.674 0.867 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (163 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.113 0.057 199.9 68: (ns/day) (hour/ns) 68: Performance: 25.877 0.927 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 24.020 0.999 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 24.087 0.996 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (147 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 24.091 0.996 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.633 1.060 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.633 1.060 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (146 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.113 0.057 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.875 0.928 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 24.028 0.999 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.066 0.033 199.7 68: (ns/day) (hour/ns) 68: Performance: 23.660 1.014 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (139 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 21.583 1.112 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.466 1.173 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.435 1.174 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (162 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 21.603 1.111 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.345 1.180 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.715 1.159 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (161 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.167 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.552 1.367 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.094 0.047 199.9 68: (ns/day) (hour/ns) 68: Performance: 16.487 1.456 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.127 0.064 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.193 1.968 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (209 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 196.4 68: (ns/day) (hour/ns) 68: Performance: 1147.438 0.021 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.103 0.052 199.9 68: (ns/day) (hour/ns) 68: Performance: 15.091 1.590 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.112 0.056 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.918 1.724 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (132 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.135 0.067 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.790 1.101 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.460 1.173 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.326 1.181 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (165 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.128 0.064 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.016 1.043 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.7 68: (ns/day) (hour/ns) 68: Performance: 21.653 1.108 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.8 68: (ns/day) (hour/ns) 68: Performance: 21.636 1.109 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (156 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.167 0.084 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.535 1.369 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.093 0.046 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.793 1.429 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.093 0.046 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.777 1.431 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (195 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.135 0.067 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.815 1.100 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.135 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.499 2.087 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.127 0.063 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.284 1.954 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (217 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.415 0.208 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.077 3.391 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.225 0.112 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.913 3.472 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.225 0.112 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.921 3.468 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (501 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.415 0.207 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.080 3.390 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.225 0.113 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.901 3.478 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.224 0.112 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.924 3.466 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (500 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.494 0.247 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.946 4.037 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.266 0.133 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.838 4.111 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.260 0.130 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.977 4.015 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (568 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.494 0.247 200.0 68: (ns/day) (hour/ns) 68: Performance: 5.950 4.034 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 199.5 68: (ns/day) (hour/ns) 68: Performance: 30.354 0.791 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.261 0.130 199.9 68: (ns/day) (hour/ns) 68: Performance: 5.960 4.027 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (460 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.420 0.210 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.989 3.434 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.233 0.117 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.664 3.602 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.229 0.115 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.788 3.535 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (516 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.405 0.203 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.247 3.312 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.231 0.115 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.735 3.563 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.219 0.110 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.085 3.387 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (571 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.684 0.342 200.0 68: (ns/day) (hour/ns) 68: Performance: 4.295 5.588 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.361 0.181 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.305 5.574 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.365 0.182 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.263 5.629 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (817 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.930 0.465 200.0 68: (ns/day) (hour/ns) 68: Performance: 3.157 7.602 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.392 0.196 199.9 68: (ns/day) (hour/ns) 68: Performance: 3.962 6.057 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.359 0.179 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.335 5.536 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (989 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (7544 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.185 0.092 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.896 1.510 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.110 0.055 199.7 68: (ns/day) (hour/ns) 68: Performance: 14.140 1.697 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.102 0.051 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.285 1.570 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (239 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.183 0.092 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.048 1.495 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.103 0.052 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.037 1.596 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.103 0.051 199.7 68: (ns/day) (hour/ns) 68: Performance: 15.131 1.586 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (235 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.264 0.132 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.110 2.160 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.177 0.088 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.788 2.731 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.128 0.064 199.7 68: (ns/day) (hour/ns) 68: Performance: 12.103 1.983 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (328 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.241 0.120 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.190 1.969 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.196 0.098 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.938 3.023 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.233 0.117 199.8 68: (ns/day) (hour/ns) 68: Performance: 6.673 3.597 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (383 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.191 0.096 199.9 68: (ns/day) (hour/ns) 68: Performance: 15.359 1.563 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.105 0.053 199.7 68: (ns/day) (hour/ns) 68: Performance: 14.769 1.625 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.691 1.891 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (286 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.420 0.210 199.9 68: (ns/day) (hour/ns) 68: Performance: 6.994 3.431 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.8 68: (ns/day) (hour/ns) 68: Performance: 11.418 2.102 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.145 0.073 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.725 2.238 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (561 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.304 0.152 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.675 2.481 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.162 0.081 199.9 68: (ns/day) (hour/ns) 68: Performance: 9.620 2.495 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.151 0.076 199.8 68: (ns/day) (hour/ns) 68: Performance: 10.267 2.338 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (438 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.217 0.108 199.9 68: (ns/day) (hour/ns) 68: Performance: 13.542 1.772 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.118 0.059 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.136 1.827 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.173 0.087 199.9 68: (ns/day) (hour/ns) 68: Performance: 8.986 2.671 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (313 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2786 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.149 0.075 199.9 68: (ns/day) (hour/ns) 68: Performance: 19.664 1.221 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 30 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.128 0.064 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.182 1.970 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.120 0.060 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.951 1.853 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (233 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.116 0.058 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.373 0.946 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.001 0.001 191.4 68: (ns/day) (hour/ns) 68: Performance: 1074.272 0.022 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.6 68: (ns/day) (hour/ns) 68: Performance: 23.973 1.001 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (105 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.8 68: (ns/day) (hour/ns) 68: Performance: 22.656 1.059 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.070 0.035 199.6 68: (ns/day) (hour/ns) 68: Performance: 22.281 1.077 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.612 1.061 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (151 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.113 0.057 199.8 68: (ns/day) (hour/ns) 68: Performance: 25.867 0.928 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.032 199.7 68: (ns/day) (hour/ns) 68: Performance: 24.020 0.999 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.065 0.033 198.1 68: (ns/day) (hour/ns) 68: Performance: 23.840 1.007 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (138 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.139 0.069 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.195 1.132 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.755 1.215 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.390 1.177 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (161 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.131 0.065 199.8 68: (ns/day) (hour/ns) 68: Performance: 22.483 1.067 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.075 0.037 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.834 1.152 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.6 68: (ns/day) (hour/ns) 68: Performance: 21.608 1.111 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (153 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.177 0.089 199.9 68: (ns/day) (hour/ns) 68: Performance: 16.570 1.448 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.101 0.051 199.9 68: (ns/day) (hour/ns) 68: Performance: 15.393 1.559 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.085 0.043 199.7 68: (ns/day) (hour/ns) 68: Performance: 18.292 1.312 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (196 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.148 0.074 199.9 68: (ns/day) (hour/ns) 68: Performance: 19.883 1.207 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.083 0.042 199.8 68: (ns/day) (hour/ns) 68: Performance: 18.687 1.284 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 68: 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.081 0.040 199.6 68: (ns/day) (hour/ns) 68: Performance: 19.205 1.250 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (172 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1314 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 24.024 0.999 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.6 68: (ns/day) (hour/ns) 68: Performance: 22.558 1.064 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.034 199.6 68: (ns/day) (hour/ns) 68: Performance: 22.658 1.059 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (147 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.139 0.070 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.099 1.138 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.739 1.216 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.325 1.181 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (162 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (310 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.123 0.062 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.862 1.006 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.607 1.062 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.034 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.599 1.062 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (148 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.125 0.063 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.427 1.024 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.035 199.7 68: (ns/day) (hour/ns) 68: Performance: 21.951 1.093 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.071 0.036 199.7 68: (ns/day) (hour/ns) 68: Performance: 21.764 1.103 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (150 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.122 0.061 199.8 68: (ns/day) (hour/ns) 68: Performance: 24.089 0.996 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.068 0.034 199.6 68: (ns/day) (hour/ns) 68: Performance: 22.801 1.053 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.069 0.035 199.7 68: (ns/day) (hour/ns) 68: Performance: 22.387 1.072 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (147 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.127 0.063 199.8 68: (ns/day) (hour/ns) 68: Performance: 23.176 1.036 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.7 68: (ns/day) (hour/ns) 68: Performance: 21.667 1.108 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.7 68: (ns/day) (hour/ns) 68: Performance: 20.348 1.179 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (154 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.140 0.070 199.9 68: (ns/day) (hour/ns) 68: Performance: 21.043 1.141 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.714 1.217 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.076 0.038 199.6 68: (ns/day) (hour/ns) 68: Performance: 20.374 1.178 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (163 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.143 0.071 199.9 68: (ns/day) (hour/ns) 68: Performance: 20.586 1.166 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.081 0.041 199.8 68: (ns/day) (hour/ns) 68: Performance: 19.188 1.251 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.039 199.6 68: (ns/day) (hour/ns) 68: Performance: 19.718 1.217 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (165 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.165 0.083 199.9 68: (ns/day) (hour/ns) 68: Performance: 17.762 1.351 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.091 0.046 199.8 68: (ns/day) (hour/ns) 68: Performance: 17.078 1.405 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.088 0.044 199.7 68: (ns/day) (hour/ns) 68: Performance: 17.550 1.367 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (188 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1118 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.267 0.133 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.009 2.180 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.145 0.072 199.9 68: (ns/day) (hour/ns) 68: Performance: 10.734 2.236 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.144 0.072 199.7 68: (ns/day) (hour/ns) 68: Performance: 10.804 2.221 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (295 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (295 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.141 0.071 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.769 1.156 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.080 0.040 199.7 68: (ns/day) (hour/ns) 68: Performance: 19.458 1.233 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 15 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.081 0.040 199.7 68: (ns/day) (hour/ns) 68: Performance: 19.276 1.245 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (173 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 66 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 199.7 68: (ns/day) (hour/ns) 68: Performance: 47.945 0.501 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 199.8 68: (ns/day) (hour/ns) 68: Performance: 15.962 1.504 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.094 0.047 199.7 68: (ns/day) (hour/ns) 68: Performance: 16.546 1.450 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (170 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (344 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to -1777338405 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -1174622401 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.175 0.088 199.8 68: (ns/day) (hour/ns) 68: Performance: 16.784 1.430 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.097 0.049 199.6 68: (ns/day) (hour/ns) 68: Performance: 15.970 1.503 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.7 68: (ns/day) (hour/ns) 68: Performance: 16.109 1.490 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (232 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to 1438640074 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -1140876323 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.215 0.108 199.8 68: (ns/day) (hour/ns) 68: Performance: 13.663 1.757 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.121 0.061 199.7 68: (ns/day) (hour/ns) 68: Performance: 12.806 1.874 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.114 0.057 199.7 68: (ns/day) (hour/ns) 68: Performance: 13.602 1.764 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (272 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (505 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.250 0.125 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.727 2.047 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.136 0.068 199.9 68: (ns/day) (hour/ns) 68: Performance: 11.466 2.093 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.130 0.065 199.7 68: (ns/day) (hour/ns) 68: Performance: 11.915 2.014 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (305 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (305 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -93360141 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 19 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.2 68: (ns/day) (hour/ns) 68: Performance: 12.688 1.892 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (24 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to 1599061907 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 199.6 68: (ns/day) (hour/ns) 68: Performance: 8.637 2.779 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (27 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI thread 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1111490725 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.019 199.4 68: (ns/day) (hour/ns) 68: Performance: 8.946 2.683 68: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (30 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (82 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (15462 ms total) 68: [ PASSED ] 76 tests. 68/92 Test #68: MdrunIOTests .............................. Passed 15.49 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -1615354077 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 34 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.538 0.269 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.819 4.981 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.633 0.317 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.092 5.865 69: [ OK ] CompelTest.SwapCanRun (958 ms) 69: [----------] 1 test from CompelTest (958 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 51 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.2 69: (ns/day) (hour/ns) 69: Performance: 15.098 1.590 69: Setting the LD random seed to -1346594 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalBondWorks (19 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 74 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.021 0.011 199.6 69: (ns/day) (hour/ns) 69: Performance: 8.194 2.929 69: Setting the LD random seed to -285475882 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (21 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 28 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.023 0.012 199.5 69: (ns/day) (hour/ns) 69: Performance: 7.485 3.206 69: Setting the LD random seed to -227025227 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (21 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 29 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.020 0.010 199.5 69: (ns/day) (hour/ns) 69: Performance: 8.612 2.787 69: Setting the LD random seed to -671389281 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (15 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 53 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.2 69: (ns/day) (hour/ns) 69: Performance: 15.192 1.580 69: Setting the LD random seed to -2621591 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (18 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.2 69: (ns/day) (hour/ns) 69: Performance: 15.059 1.594 69: Setting the LD random seed to 1471412583 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (15 ms) 69: [----------] 6 tests from BondedInteractionsTest (111 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: 69: NOTE: 41 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.014 0.007 198.8 69: (ns/day) (hour/ns) 69: Performance: 23.833 1.007 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -402670097 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to -1342440467 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (14 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: Setting the LD random seed to 2138045613 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.18 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.694 0.347 200.0 69: (ns/day) (hour/ns) 69: Performance: 10.449 2.297 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (772 ms) 69: [----------] 2 tests from BoxDeformationTest (787 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to 1990807003 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: This run will generate roughly 1 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.047 0.523 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.632 6.608 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1036 ms) 69: [----------] 1 test from PositionRestraintCommTest (1036 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -25333778 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in domain decomposition, 69: 6 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.109 0.055 199.8 69: (ns/day) (hour/ns) 69: Performance: 7.890 3.042 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -4727842 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 16 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.100 0.050 199.8 69: (ns/day) (hour/ns) 69: Performance: 8.646 2.776 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (164 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to 2011168697 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.106 0.053 199.8 69: (ns/day) (hour/ns) 69: Performance: 8.137 2.950 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -218286085 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 16 % of the run time was spent in domain decomposition, 69: 5 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.094 0.047 199.7 69: (ns/day) (hour/ns) 69: Performance: 9.174 2.616 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (155 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (320 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -403833091 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 25 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.087 0.043 199.7 69: (ns/day) (hour/ns) 69: Performance: 9.932 2.417 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: Setting the LD random seed to -1083393 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 27 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.086 0.043 199.7 69: (ns/day) (hour/ns) 69: Performance: 10.004 2.399 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (118 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (118 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.098 0.049 199.8 69: (ns/day) (hour/ns) 69: Performance: 15.834 1.516 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (65 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.095 0.047 199.7 69: (ns/day) (hour/ns) 69: Performance: 16.415 1.462 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (64 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.093 0.046 199.8 69: (ns/day) (hour/ns) 69: Performance: 16.758 1.432 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (62 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.120 0.060 199.8 69: (ns/day) (hour/ns) 69: Performance: 12.943 1.854 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (75 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.123 0.062 199.8 69: (ns/day) (hour/ns) 69: Performance: 12.624 1.901 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (80 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.118 0.059 199.8 69: (ns/day) (hour/ns) 69: Performance: 13.113 1.830 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (78 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.118 0.059 199.8 69: (ns/day) (hour/ns) 69: Performance: 13.122 1.829 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (78 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.157 0.079 199.8 69: (ns/day) (hour/ns) 69: Performance: 9.878 2.430 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (103 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.140 0.070 199.8 69: (ns/day) (hour/ns) 69: Performance: 11.112 2.160 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (138 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.135 0.068 199.8 69: (ns/day) (hour/ns) 69: Performance: 11.498 2.087 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (130 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 11 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.133 0.066 199.8 69: (ns/day) (hour/ns) 69: Performance: 11.698 2.052 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (129 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1008 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -41943299 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.108 0.054 199.8 69: (ns/day) (hour/ns) 69: Performance: 28.679 0.837 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (71 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -201589801 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.111 0.056 199.8 69: (ns/day) (hour/ns) 69: Performance: 27.876 0.861 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (66 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -131077 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.102 0.051 199.8 69: (ns/day) (hour/ns) 69: Performance: 30.411 0.789 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (61 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -28312802 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 10 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.117 0.059 199.8 69: (ns/day) (hour/ns) 69: Performance: 26.558 0.904 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (65 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (265 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (4673 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/92 Test #69: MdrunTestsOneRank ......................... Passed 4.69 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Generating 1-4 interactions: fudge = 0.5 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to 1556016126 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 12.8%. 70: The balanceable part of the MD step is 26%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 3.4%. 70: 70: 70: NOTE: 40 % of the run time was spent in domain decomposition, 70: 8 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.513 0.878 400.0 70: (ns/day) (hour/ns) 70: Performance: 1.476 16.265 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.040 0.760 399.9 70: (ns/day) (hour/ns) 70: Performance: 1.705 14.078 70: [ OK ] CompelTest.SwapCanRun (3181 ms) 70: [----------] 1 test from CompelTest (3181 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 43 % of the run time was spent in domain decomposition, 70: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.214 0.053 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.615 14.856 70: Setting the LD random seed to -1199898693 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalBondWorks (155 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 50 % of the run time was spent in domain decomposition, 70: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.190 0.047 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.819 13.192 70: Setting the LD random seed to 964639647 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (148 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 36 % of the run time was spent in domain decomposition, 70: 22 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.093 0.023 399.5 70: (ns/day) (hour/ns) 70: Performance: 3.694 6.497 70: Setting the LD random seed to -27263621 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (92 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 40 % of the run time was spent in domain decomposition, 70: 44 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.108 0.027 399.6 70: (ns/day) (hour/ns) 70: Performance: 3.208 7.482 70: Setting the LD random seed to -631409192 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (69 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 75 % of the run time was spent in domain decomposition, 70: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.253 0.063 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.367 17.554 70: Setting the LD random seed to 1537884135 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (190 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 58 % of the run time was spent in domain decomposition, 70: 9 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.235 0.059 399.8 70: (ns/day) (hour/ns) 70: Performance: 1.469 16.342 70: Setting the LD random seed to -1624266121 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (135 ms) 70: [----------] 6 tests from BondedInteractionsTest (791 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 43 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 17 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.173 0.043 399.2 70: (ns/day) (hour/ns) 70: Performance: 3.985 6.023 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1945759603 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to -276873225 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (86 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: Setting the LD random seed to 2142231010 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.18 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.7%. 70: The balanceable part of the MD step is 23%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.5%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.478 0.370 399.9 70: (ns/day) (hour/ns) 70: Performance: 9.820 2.444 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1392 ms) 70: [----------] 2 tests from BoxDeformationTest (1478 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: Setting the LD random seed to -25203271 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.766 0.942 400.0 70: (ns/day) (hour/ns) 70: Performance: 2.019 11.889 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (2051 ms) 70: [----------] 1 test from PositionRestraintCommTest (2051 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1740369790 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.507 0.127 399.8 70: (ns/day) (hour/ns) 70: Performance: 3.409 7.040 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1879048191 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 8 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.265 0.066 399.6 70: (ns/day) (hour/ns) 70: Performance: 6.518 3.682 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1197 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -1073742337 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 9 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 3.688 0.952 387.4 70: (ns/day) (hour/ns) 70: Performance: 0.454 52.887 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -142868548 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 5 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.539 0.635 400.0 70: (ns/day) (hour/ns) 70: Performance: 0.680 35.273 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (3859 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (5056 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to -404021275 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.232 0.308 399.9 70: (ns/day) (hour/ns) 70: Performance: 1.402 17.117 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Setting the LD random seed to 1844375551 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.007 0.252 399.9 70: (ns/day) (hour/ns) 70: Performance: 1.715 13.996 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (1580 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (1589 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 2.7%. 70: The balanceable part of the MD step is 51%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.4%. 70: 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.583 0.146 399.8 70: (ns/day) (hour/ns) 70: Performance: 5.334 4.499 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (332 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 32.9%. 70: The balanceable part of the MD step is 40%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 13.2%. 70: 70: NOTE: 13.2 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 3 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.067 0.542 381.5 70: (ns/day) (hour/ns) 70: Performance: 1.435 16.723 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1644 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 36.2%. 70: The balanceable part of the MD step is 41%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 14.8%. 70: 70: NOTE: 14.8 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 14 % of the run time was spent in domain decomposition, 70: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.744 0.186 399.8 70: (ns/day) (hour/ns) 70: Performance: 4.181 5.740 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (295 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 25.3%. 70: The balanceable part of the MD step is 42%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 10.7%. 70: 70: NOTE: 10.7 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 19 % of the run time was spent in domain decomposition, 70: 2 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 19 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.400 0.616 389.6 70: (ns/day) (hour/ns) 70: Performance: 1.263 19.009 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1392 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.1%. 70: The balanceable part of the MD step is 57%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 3.5%. 70: 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 9 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.715 0.183 391.0 70: (ns/day) (hour/ns) 70: Performance: 4.254 5.641 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (515 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 70: Parrinello-Rahman is not implemented in md-vv. 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.002 0.516 388.0 70: (ns/day) (hour/ns) 70: Performance: 1.507 15.922 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (1252 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.037 0.259 399.9 70: (ns/day) (hour/ns) 70: Performance: 2.999 8.002 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (352 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in domain decomposition, 70: 1 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 18 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.866 0.744 385.2 70: (ns/day) (hour/ns) 70: Performance: 1.045 22.959 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1958 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 8 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.224 0.306 399.9 70: (ns/day) (hour/ns) 70: Performance: 2.541 9.445 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (931 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in domain decomposition, 70: 0 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 12 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.362 0.612 385.9 70: (ns/day) (hour/ns) 70: Performance: 1.271 18.889 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1764 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 70: 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 8 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.898 0.225 399.8 70: (ns/day) (hour/ns) 70: Performance: 3.463 6.931 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (359 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (10808 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -537398309 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 20.2%. 70: The balanceable part of the MD step is 35%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 7.2%. 70: 70: NOTE: 7.2 % of the available CPU time was lost due to load imbalance 70: in the domain decomposition. 70: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 70: You can also consider manually changing the decomposition (option -dd); 70: e.g. by using fewer domains along the box dimension in which there is 70: considerable inhomogeneity in the simulated system. 70: 70: NOTE: 34 % of the run time was spent in domain decomposition, 70: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.518 0.130 399.8 70: (ns/day) (hour/ns) 70: Performance: 12.000 2.000 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (314 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 518978813 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 9.6%. 70: The balanceable part of the MD step is 27%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.6%. 70: 70: 70: NOTE: 28 % of the run time was spent in domain decomposition, 70: 6 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 11 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.315 0.329 399.9 70: (ns/day) (hour/ns) 70: Performance: 4.731 5.073 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (545 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -68227363 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.5%. 70: The balanceable part of the MD step is 45%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.2%. 70: 70: 70: NOTE: 24 % of the run time was spent in domain decomposition, 70: 5 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 14 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 1.608 0.442 363.8 70: (ns/day) (hour/ns) 70: Performance: 3.519 6.821 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (795 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI threads 70: Using 2 OpenMP threads per tMPI thread 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -820237 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.4%. 70: The balanceable part of the MD step is 41%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.6%. 70: 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 4 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 16 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 2.321 0.580 400.0 70: (ns/day) (hour/ns) 70: Performance: 2.680 8.955 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (895 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (2552 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (27588 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/92 Test #70: MdrunTestsTwoRanks ........................ Passed 27.62 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to -272631987 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 4.426 2.213 200.0 71: (ns/day) (hour/ns) 71: Performance: 15.693 1.529 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (2295 ms) 71: [----------] 1 test from DispersionCorrectionTest (2295 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 71: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 71: 71: 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to -1006765195 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.241 0.121 199.9 71: (ns/day) (hour/ns) 71: Performance: 15.745 1.524 71: [ OK ] OriresTest.OriresCanRun (1049 ms) 71: [----------] 1 test from OriresTest (1049 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -859832586 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.672 0.336 200.0 71: (ns/day) (hour/ns) 71: Performance: 13.498 1.778 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (399 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI thread 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to 1939593695 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.765 0.383 200.0 71: (ns/day) (hour/ns) 71: Performance: 11.858 2.024 71: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (417 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (816 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (4212 ms total) 71: [ PASSED ] 5 tests. 71/92 Test #71: MdrunSingleRankAlgorithmsTests ............ Passed 4.24 sec test 72 Start 72: Minimize1RankTests 72: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.79910463671092e+01 72: Maximum force = 1.86297359432231e+02 on atom 13 72: Norm of force = 8.77219865482157e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (912 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.58622538633302e+01 72: Maximum force = 4.27274822366368e+02 on atom 13 72: Norm of force = 1.84530029253754e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1080 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.19376899751523e+02 72: Maximum force = 9.99884921009767e+03 on atom 9 72: Norm of force = 4.61669565054298e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (293 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.51743018140928e+02 72: Maximum force = 7.42089573409108e+03 on atom 9 72: Norm of force = 3.56929298615740e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (344 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.56984193848274e+02 72: Maximum force = 4.56923624626570e+02 on atom 17 72: Norm of force = 1.83258377168389e+02 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (138 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06800e+03 on atom 28 72: F-Norm = 4.26922e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.69410778678181e+02 72: Maximum force = 2.18225948473987e+02 on atom 17 72: Norm of force = 7.92068036537548e+01 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (133 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2903 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.74257075835447e-01 72: Maximum force = 4.01322929015133e+00 on atom 1 72: Norm of force = 1.63839399694378e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (11 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.90642313893957e-01 72: Maximum force = 2.57812909491104e+00 on atom 1 72: Norm of force = 1.05251679559258e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (60 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.90642313893957e-01 72: Maximum force = 2.57812909491104e+00 on atom 1 72: Norm of force = 1.05251679559258e+00 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.19395484891520e+02 72: Maximum force = 9.97041707197911e+03 on atom 9 72: Norm of force = 4.62274878665467e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (240 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.56258793899480e+02 72: Maximum force = 7.50181017480397e+03 on atom 9 72: Norm of force = 3.61390332564874e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (247 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Generating 1-4 interactions: fudge = 1 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 72: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.61116097794205e+02 72: Maximum force = 1.26854826291223e+04 on atom 10 72: Norm of force = 6.06436286976271e+03 72: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (233 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (817 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (3759 ms total) 72: [ PASSED ] 12 tests. 72/92 Test #72: Minimize1RankTests ........................ Passed 3.80 sec test 73 Start 73: Minimize2RankTests 73: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.79910463671093e+01 73: Maximum force = 1.86297359432232e+02 on atom 13 73: Norm of force = 8.77219865482159e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1803 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.58622538633302e+01 73: Maximum force = 4.27274822366367e+02 on atom 13 73: Norm of force = 1.84530029253753e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1407 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.19376899751523e+02 73: Maximum force = 9.99884921009767e+03 on atom 9 73: Norm of force = 4.61669565054298e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1200 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.51743018140927e+02 73: Maximum force = 7.42089573409111e+03 on atom 9 73: Norm of force = 3.56929298615739e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (3011 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.56984193848274e+02 73: Maximum force = 4.56923624626570e+02 on atom 17 73: Norm of force = 1.83258377168389e+02 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1041 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 0.5 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06800e+03 on atom 28 73: F-Norm = 4.26922e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.69410778678181e+02 73: Maximum force = 2.18225948473987e+02 on atom 17 73: Norm of force = 7.92068036537548e+01 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (3247 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (11711 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.74257075835447e-01 73: Maximum force = 4.01322929015133e+00 on atom 3 73: Norm of force = 1.63839399694378e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (253 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.90642313893957e-01 73: Maximum force = 2.57812909491104e+00 on atom 3 73: Norm of force = 1.05251679559258e+00 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (1679 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.19395484891520e+02 73: Maximum force = 9.97041707197911e+03 on atom 9 73: Norm of force = 4.62274878665467e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1481 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 73: Using 2 MPI threads 73: Using 2 OpenMP threads per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.56258793899480e+02 73: Maximum force = 7.50181017480397e+03 on atom 9 73: Norm of force = 3.61390332564874e+03 73: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (683 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generating 1-4 interactions: fudge = 1 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (116 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (4216 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (15962 ms total) 73: [ PASSED ] 12 tests. 73/92 Test #73: Minimize2RankTests ........................ Passed 16.02 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 53 tests from 5 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: SIMD width: 2 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. 4xM 0.840 0.8399 1.2616 0.7498 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (90 ms) 74: [----------] 1 test from NonbondedBenchTest (90 ms total) 74: 74: [----------] 5 tests from NormalModesWorks/NormalModesTest 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation '2 scaled waters' 74: 12 steps. 74: 74: Maximum force: 9.96989e-06 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (311 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 1 74: 74: NOTE 3 [file villin.top, line 2452]: 74: System has non-zero total charge: -2.000000 74: Total charge should normally be an integer. See 74: https://manual.gromacs.org/current/user-guide/floating-point.html 74: for discussion on how close it should be to an integer. 74: 74: 74: 74: Number of degrees of freedom in T-Coupling group System is 765.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=256), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 74: 512 steps. 74: 74: Maximum force: 6.97568e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 50... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--50 to eigenvec.trr 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 256 Atoms 74: Using begin = 7 and end = 50 74: Full matrix storage format, nrow=768, ncols=768 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (9879 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'flex spc dimer' 74: 12 steps. 74: 74: Maximum force: 3.36401e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (1090 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 6.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=3), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation '1 TIP5P' 74: 6 steps. 74: 74: Maximum force: 2.42882e-04 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 9... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--9 to eigenvec.trr 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: This run will generate roughly 0 Mb of data 74: There are: 3 Atoms 74: There are: 2 VSites 74: Using begin = 7 and end = 9 74: Full matrix storage format, nrow=9, ncols=9 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (965 ms) 74: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: Number of degrees of freedom in T-Coupling group System is 15.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Small system size (N=6), using full Hessian format. 74: Allocating Hessian memory... 74: 74: starting normal mode calculation 'sw dimer' 74: 12 steps. 74: 74: Maximum force: 1.07599e-03 74: The force is probably not small enough to ensure that you are at a minimum. 74: Be aware that negative eigenvalues may occur 74: when the resulting matrix is diagonalized. 74: 74: 74: Writing Hessian... 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Reading double precision matrix generated by GROMACS 2025.1-Debian_2025.1_1 74: 74: Diagonalizing to find vectors 7 through 18... 74: Writing eigenvalues... 74: 74: Writing average structure & eigenvectors 7--18 to eigenvec.trr 74: Generated 6 of the 10 non-bonded parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SW' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: This run will generate roughly 0 Mb of data 74: There are: 6 Atoms 74: There are: 2 Shells 74: There are: 2 VSites 74: 74: NOTE: in the current version shell prediction during the crun is disabled 74: 74: Using begin = 7 and end = 18 74: Full matrix storage format, nrow=18, ncols=18 74: Writing eigenfrequencies - negative eigenvalues will be set to zero. 74: Cannot compute entropy when -first = 7 74: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (326 ms) 74: [----------] 5 tests from NormalModesWorks/NormalModesTest (12574 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.185 0.093 199.9 74: (ns/day) (hour/ns) 74: Performance: 15.833 1.516 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (double precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.070 0.035 199.8 74: (ns/day) (hour/ns) 74: Performance: 41.757 0.575 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (150 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.210 0.105 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.956 1.720 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 75 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.036 199.8 74: (ns/day) (hour/ns) 74: Performance: 40.360 0.595 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (161 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.176 0.088 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.667 1.440 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 45 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.081 0.041 199.8 74: (ns/day) (hour/ns) 74: Performance: 36.134 0.664 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (145 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.175 0.087 199.9 74: (ns/day) (hour/ns) 74: Performance: 16.800 1.429 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 40 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.073 0.036 199.8 74: (ns/day) (hour/ns) 74: Performance: 40.292 0.596 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (143 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.284 0.142 199.9 74: (ns/day) (hour/ns) 74: Performance: 10.338 2.322 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 57 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.069 0.034 199.8 74: (ns/day) (hour/ns) 74: Performance: 42.722 0.562 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (753 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.480 0.240 200.0 74: (ns/day) (hour/ns) 74: Performance: 6.119 3.922 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 43 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.033 199.8 74: (ns/day) (hour/ns) 74: Performance: 45.057 0.533 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (836 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.260 0.130 199.9 74: (ns/day) (hour/ns) 74: Performance: 11.288 2.126 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 57 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.095 0.048 199.9 74: (ns/day) (hour/ns) 74: Performance: 30.878 0.777 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (1124 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.341 0.170 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.619 2.784 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 78 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.099 0.050 199.9 74: (ns/day) (hour/ns) 74: Performance: 29.617 0.810 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1137 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.662 0.331 200.0 74: (ns/day) (hour/ns) 74: Performance: 4.437 5.409 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 67 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.098 0.049 199.8 74: (ns/day) (hour/ns) 74: Performance: 29.917 0.802 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (459 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.783 0.392 200.0 74: (ns/day) (hour/ns) 74: Performance: 3.749 6.401 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 49 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.129 0.065 199.9 74: (ns/day) (hour/ns) 74: Performance: 22.717 1.056 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (523 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.671 0.335 200.0 74: (ns/day) (hour/ns) 74: Performance: 4.378 5.482 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 47 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.070 0.035 199.8 74: (ns/day) (hour/ns) 74: Performance: 41.803 0.574 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (535 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.981 0.490 200.0 74: (ns/day) (hour/ns) 74: Performance: 2.995 8.013 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 30 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.109 0.055 199.9 74: (ns/day) (hour/ns) 74: Performance: 26.860 0.894 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (642 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (6614 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.282 0.141 199.9 74: (ns/day) (hour/ns) 74: Performance: 10.424 2.302 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.100 0.050 199.8 74: (ns/day) (hour/ns) 74: Performance: 29.395 0.816 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (228 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.278 0.139 199.9 74: (ns/day) (hour/ns) 74: Performance: 10.543 2.276 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 66 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.081 0.040 199.8 74: (ns/day) (hour/ns) 74: Performance: 36.418 0.659 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (225 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.196 0.098 199.8 74: (ns/day) (hour/ns) 74: Performance: 14.997 1.600 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.752 0.492 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (169 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.183 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.053 1.495 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.451 0.495 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (146 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.183 0.092 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.997 1.500 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 47.834 0.502 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (147 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.184 0.092 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.981 1.502 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.211 0.488 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (147 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.181 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.174 1.484 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 49.059 0.489 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (144 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.182 0.091 199.8 74: (ns/day) (hour/ns) 74: Performance: 16.138 1.487 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.499 0.495 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (145 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.183 0.092 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.998 1.500 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 54 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.462 0.495 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (147 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.184 0.092 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.987 1.501 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.062 0.031 199.7 74: (ns/day) (hour/ns) 74: Performance: 47.454 0.506 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (148 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.226 0.113 199.8 74: (ns/day) (hour/ns) 74: Performance: 12.980 1.849 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.359 0.496 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (168 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.231 0.116 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.688 1.892 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.061 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.474 0.495 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (167 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.232 0.116 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.685 1.892 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.595 0.494 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (167 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.232 0.116 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.673 1.894 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 55 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.060 0.030 199.7 74: (ns/day) (hour/ns) 74: Performance: 48.646 0.493 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (168 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.232 0.116 199.9 74: (ns/day) (hour/ns) 74: Performance: 12.676 1.893 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 58 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.094 0.047 199.8 74: (ns/day) (hour/ns) 74: Performance: 31.182 0.770 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (190 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.345 0.173 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.504 2.822 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.101 0.050 199.8 74: (ns/day) (hour/ns) 74: Performance: 29.125 0.824 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (264 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.355 0.178 200.0 74: (ns/day) (hour/ns) 74: Performance: 8.268 2.903 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.092 0.046 199.8 74: (ns/day) (hour/ns) 74: Performance: 31.991 0.750 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (264 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.352 0.176 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.338 2.878 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 64 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.103 0.052 199.8 74: (ns/day) (hour/ns) 74: Performance: 28.477 0.843 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (264 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.354 0.177 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.299 2.892 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 64 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.102 0.051 199.8 74: (ns/day) (hour/ns) 74: Performance: 28.703 0.836 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (263 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.383 0.191 200.0 74: (ns/day) (hour/ns) 74: Performance: 7.672 3.128 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.088 0.044 199.8 74: (ns/day) (hour/ns) 74: Performance: 33.392 0.719 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (280 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.351 0.175 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.376 2.865 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 53 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.093 0.047 199.8 74: (ns/day) (hour/ns) 74: Performance: 31.492 0.762 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (262 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.363 0.181 200.0 74: (ns/day) (hour/ns) 74: Performance: 8.096 2.964 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 56 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.092 0.046 199.8 74: (ns/day) (hour/ns) 74: Performance: 31.775 0.755 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (270 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.215 0.108 199.8 74: (ns/day) (hour/ns) 74: Performance: 13.650 1.758 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.342 0.529 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (181 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.214 0.107 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.711 1.750 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.691 0.525 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.216 0.108 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.608 1.764 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.066 0.033 199.7 74: (ns/day) (hour/ns) 74: Performance: 44.672 0.537 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.215 0.108 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.643 1.759 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 51 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.420 0.528 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.214 0.107 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.688 1.753 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.525 0.527 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (173 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.215 0.107 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.665 1.756 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.767 0.524 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (172 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.310 0.155 199.9 74: (ns/day) (hour/ns) 74: Performance: 9.466 2.535 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.064 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.478 0.528 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (229 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.217 0.108 199.9 74: (ns/day) (hour/ns) 74: Performance: 13.554 1.771 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 52 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.065 0.032 199.7 74: (ns/day) (hour/ns) 74: Performance: 45.419 0.528 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (174 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.415 0.207 199.9 74: (ns/day) (hour/ns) 74: Performance: 7.081 3.389 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 49 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.425 0.213 200.0 74: (ns/day) (hour/ns) 74: Performance: 6.907 3.475 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (519 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.056 0.028 199.5 74: (ns/day) (hour/ns) 74: Performance: 52.415 0.458 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 61 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.142 0.071 199.9 74: (ns/day) (hour/ns) 74: Performance: 20.629 1.163 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (215 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.348 0.174 199.9 74: (ns/day) (hour/ns) 74: Performance: 8.430 2.847 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 74: 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 40 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.087 0.043 199.8 74: (ns/day) (hour/ns) 74: Performance: 33.904 0.708 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (269 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (6841 ms total) 74: 74: [----------] 2 tests from Angles1/SimpleMdrunTest 74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file angles1.top, line 72]: 74: In moleculetype 'butane' 4 atoms are not bound by a potential or 74: constraint to any other atom in the same moleculetype. Although 74: technically this might not cause issues in a simulation, this often means 74: that the user forgot to add a bond/potential/constraint or put multiple 74: molecules in the same moleculetype definition by mistake. Run with -v to 74: get information for each atom. 74: 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 238.919 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'This_incredible_box_of_butane' 74: 50 steps, 0.1 ps. 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'butane' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.424 0.212 199.9 74: (ns/day) (hour/ns) 74: Performance: 20.789 1.154 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (223 ms) 74: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file angles1.top, line 72]: 74: In moleculetype 'butane' 4 atoms are not bound by a potential or 74: constraint to any other atom in the same moleculetype. Although 74: technically this might not cause issues in a simulation, this often means 74: that the user forgot to add a bond/potential/constraint or put multiple 74: molecules in the same moleculetype definition by mistake. Run with -v to 74: get information for each atom. 74: 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 238.919 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'This_incredible_box_of_butane' 74: 50 steps, 0.1 ps. 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'butane' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.878 0.439 200.0 74: (ns/day) (hour/ns) 74: Performance: 10.033 2.392 74: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 74: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (455 ms) 74: [----------] 2 tests from Angles1/SimpleMdrunTest (679 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 53 tests from 5 test suites ran. (26870 ms total) 74: [ PASSED ] 53 tests. 74/92 Test #74: MdrunNonIntegratorTests ................... Passed 26.90 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (627 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (621 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI thread 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (674 ms) 75: [----------] 3 tests from Simple/TpiTest (1923 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (1931 ms total) 75: [ PASSED ] 3 tests. 75/92 Test #75: MdrunTpiTests ............................. Passed 1.98 sec test 76 Start 76: MdrunMpiTests 76: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 78 % of the run time was spent in domain decomposition, 76: 3 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 11 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.070 0.287 372.3 76: (ns/day) (hour/ns) 76: Performance: 0.301 79.856 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -67111116 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.OneQuantumMol (854 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 81 % of the run time was spent in domain decomposition, 76: 3 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.086 0.284 383.1 76: (ns/day) (hour/ns) 76: Performance: 0.305 78.760 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1044052351 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.AllQuantumMol (1175 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 66 % of the run time was spent in domain decomposition, 76: 17 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.204 0.051 399.8 76: (ns/day) (hour/ns) 76: Performance: 1.693 14.178 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2109184702 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.TwoQuantumMol (175 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 57 % of the run time was spent in domain decomposition, 76: 9 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.115 0.029 399.7 76: (ns/day) (hour/ns) 76: Performance: 2.999 8.002 76: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -494927905 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: [ OK ] MimicTest.BondCuts (115 ms) 76: [----------] 4 tests from MimicTest (2322 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: Setting the LD random seed to -142911139 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -269852683 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 1454995677 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 2144970683 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 16.1%. 76: The balanceable part of the MD step is 42%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 6.8%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: NOTE: 6.8 % of the available CPU time was lost due to load imbalance 76: in the domain decomposition. 76: You can consider manually changing the decomposition (option -dd); 76: e.g. by using fewer domains along the box dimension in which there is 76: considerable inhomogeneity in the simulated system. 76: 76: NOTE: 13 % of the run time was spent in domain decomposition, 76: 4 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 20 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 2.698 0.676 398.8 76: (ns/day) (hour/ns) 76: Performance: 2.682 8.947 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (823 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 13 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.087 0.272 399.8 76: (ns/day) (hour/ns) 76: Performance: 6.672 3.597 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (383 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot have separate PME ranks when PME is not used 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 35.0%. 76: The balanceable part of the MD step is 12%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 4.1%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: Core t (s) Wall t (s) (%) 76: Time: 7.145 1.790 399.1 76: (ns/day) (hour/ns) 76: Performance: 1.013 23.682 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (2784 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 2.966 0.765 387.4 76: (ns/day) (hour/ns) 76: Performance: 2.371 10.124 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1603 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 5.284 1.340 394.3 76: (ns/day) (hour/ns) 76: Performance: 1.354 17.724 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1799 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.748 0.438 399.1 76: (ns/day) (hour/ns) 76: Performance: 4.143 5.792 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (564 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 76: Test configuration is invalid: 76: Cannot use two separate PME ranks when there are less than four ranks total 76: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (7959 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (10326 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/92 Test #76: MdrunMpiTests ............................. Passed 10.35 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 2 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 2 tests from 1 test suite ran. (15 ms total) 77: [ PASSED ] 2 tests. 77: 77: YOU HAVE 4 DISABLED TESTS 77: 77/92 Test #77: MdrunMultiSimTests ........................ Passed 0.04 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (15 ms total) 78: [ PASSED ] 1 test. 78: 78: YOU HAVE 4 DISABLED TESTS 78: 78/92 Test #78: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 0 tests from 0 test suites. 79: [==========] 0 tests from 0 test suites ran. (0 ms total) 79: [ PASSED ] 0 tests. 79: 79: YOU HAVE 10 DISABLED TESTS 79: 79/92 Test #79: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Setting the LD random seed to -134350337 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to 531602590 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.655 0.328 200.0 80: (ns/day) (hour/ns) 80: Performance: 5.540 4.332 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (364 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.644 0.322 200.0 80: (ns/day) (hour/ns) 80: Performance: 5.635 4.259 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (353 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 35 % of the run time was spent in domain decomposition, 80: 7 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.063 0.032 199.6 80: (ns/day) (hour/ns) 80: Performance: 2.732 8.783 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (77 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.660 0.330 199.8 80: (ns/day) (hour/ns) 80: Performance: 5.494 4.369 80: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (358 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Double-precision build of GROMACS. 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (1155 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (1174 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/92 Test #80: MdrunMpi1RankPmeTests ..................... Passed 1.20 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: Setting the LD random seed to 2127291895 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Setting the LD random seed to 2146361278 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 7.8%. 81: The balanceable part of the MD step is 27%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.1%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: NOTE: 13 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 3.134 0.783 400.0 81: (ns/day) (hour/ns) 81: Performance: 2.316 10.363 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (925 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 7.1%. 81: The balanceable part of the MD step is 27%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.9%. 81: 81: 81: NOTE: 10 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 3.328 0.832 400.0 81: (ns/day) (hour/ns) 81: Performance: 2.181 11.006 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (967 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 31 % of the run time was spent in domain decomposition, 81: 5 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 7 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.336 0.084 399.1 81: (ns/day) (hour/ns) 81: Performance: 1.027 23.368 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (223 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.590 0.397 399.9 81: (ns/day) (hour/ns) 81: Performance: 4.565 5.257 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (508 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 2.067 0.517 399.9 81: (ns/day) (hour/ns) 81: Performance: 3.510 6.838 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (695 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: NOTE: 21 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.143 0.059 244.2 81: (ns/day) (hour/ns) 81: Performance: 1.471 16.316 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (552 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 2 OpenMP threads per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 26.0%. 81: The balanceable part of the MD step is 19%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 5.0%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: NOTE: 5.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: You can consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 12 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 8.593 2.148 400.0 81: (ns/day) (hour/ns) 81: Performance: 0.845 28.418 81: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (3003 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 81: Test is being skipped because: 81: it targets GPU execution, but no compatible devices were detected 81: it targets PME decomposition, but that is not supported 81: PME GPU does not support: 81: Double-precision build of GROMACS. 81: Non-GPU build of GROMACS. 81: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (6878 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (6903 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/92 Test #81: MdrunMpi2RankPmeTests ..................... Passed 6.93 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.002 98.3 82: (ns/day) (hour/ns) 82: Performance: 736.737 0.033 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.8 82: (ns/day) (hour/ns) 82: Performance: 2163.130 0.011 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.5 82: (ns/day) (hour/ns) 82: Performance: 2691.391 0.009 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.7 82: (ns/day) (hour/ns) 82: Performance: 2424.476 0.010 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2470.166 0.010 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 95.6 82: (ns/day) (hour/ns) 82: Performance: 2548.860 0.009 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (48 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (48 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (64 ms total) 82: [ PASSED ] 1 test. 82/92 Test #82: MdrunCoordinationBasicTests1Rank .......... Passed 0.08 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 53%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 37 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.004 0.002 195.4 83: (ns/day) (hour/ns) 83: Performance: 792.461 0.030 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 2%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: NOTE: 92 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.011 199.2 83: (ns/day) (hour/ns) 83: Performance: 130.714 0.184 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 28 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.6 83: (ns/day) (hour/ns) 83: Performance: 1963.223 0.012 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.0%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.7 83: (ns/day) (hour/ns) 83: Performance: 1936.076 0.012 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.5 83: (ns/day) (hour/ns) 83: Performance: 1918.590 0.013 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.6%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 190.1 83: (ns/day) (hour/ns) 83: Performance: 1885.992 0.013 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (971 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (971 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (1007 ms total) 83: [ PASSED ] 1 test. 83/92 Test #83: MdrunCoordinationBasicTests2Ranks ......... Passed 1.04 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.6 84: (ns/day) (hour/ns) 84: Performance: 146.618 0.164 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 2192.382 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2514.528 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1726.624 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2448.567 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2433.094 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (50 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1826.443 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1968.870 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1934.860 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2330.028 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2349.578 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2385.054 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (45 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1404.924 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1696.199 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2316.013 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2422.569 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.3 84: (ns/day) (hour/ns) 84: Performance: 2232.908 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 1791.912 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (53 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1813.540 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2136.128 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2580.894 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 2145.054 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.6 84: (ns/day) (hour/ns) 84: Performance: 164.462 0.146 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2291.888 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (53 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1923.382 0.012 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2235.339 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2540.451 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2263.260 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2361.285 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2373.110 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (49 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1810.874 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2097.580 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2407.422 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.5 84: (ns/day) (hour/ns) 84: Performance: 163.859 0.146 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.5 84: (ns/day) (hour/ns) 84: Performance: 2297.872 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2282.547 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (67 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 82.7 84: (ns/day) (hour/ns) 84: Performance: 1495.290 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.8 84: (ns/day) (hour/ns) 84: Performance: 1855.042 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2545.700 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2316.013 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2220.034 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1850.584 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (49 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1839.532 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2094.016 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2407.422 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1542.848 0.016 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2388.753 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2433.094 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1735.379 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1336.644 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2713.918 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2419.715 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.7 84: (ns/day) (hour/ns) 84: Performance: 2391.535 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 1590.241 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1883.398 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2239.402 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2531.057 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1115.040 0.022 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2398.051 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2415.919 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1860.644 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1713.656 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 94.9 84: (ns/day) (hour/ns) 84: Performance: 2523.799 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2278.326 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 1580.450 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2275.801 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1856.160 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2204.937 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1202.771 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2412.135 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.6 84: (ns/day) (hour/ns) 84: Performance: 2241.031 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2364.911 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1379.134 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2029.850 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 2531.057 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2219.234 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2434.055 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2452.466 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1846.701 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.7 84: (ns/day) (hour/ns) 84: Performance: 1075.710 0.022 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2549.915 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 2218.435 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1324.574 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2354.967 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1824.280 0.013 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1903.180 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2399.920 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2316.884 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.3 84: (ns/day) (hour/ns) 84: Performance: 2127.277 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2257.455 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1713.656 0.014 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 2076.371 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 2488.123 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2278.326 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.8 84: (ns/day) (hour/ns) 84: Performance: 2245.933 0.011 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1457.094 0.016 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1510.320 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1735.379 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1781.033 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1788.790 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1830.242 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.9 84: (ns/day) (hour/ns) 84: Performance: 1194.840 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (31 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.5 84: (ns/day) (hour/ns) 84: Performance: 1442.424 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1640.201 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.005 99.4 84: (ns/day) (hour/ns) 84: Performance: 288.647 0.083 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.4 84: (ns/day) (hour/ns) 84: Performance: 1753.656 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1826.443 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1824.280 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (34 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1258.805 0.019 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1704.175 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1937.294 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1822.122 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.2 84: (ns/day) (hour/ns) 84: Performance: 1830.242 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.6 84: (ns/day) (hour/ns) 84: Performance: 160.265 0.150 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (57 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.6 84: (ns/day) (hour/ns) 84: Performance: 1600.570 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1842.283 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 2031.858 0.012 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.2 84: (ns/day) (hour/ns) 84: Performance: 1849.473 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.7 84: (ns/day) (hour/ns) 84: Performance: 1776.923 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.3 84: (ns/day) (hour/ns) 84: Performance: 1907.305 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (49 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1559.644 0.015 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1718.436 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.3 84: (ns/day) (hour/ns) 84: Performance: 1250.374 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1800.817 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.0 84: (ns/day) (hour/ns) 84: Performance: 1826.985 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1758.662 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (42 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1501.485 0.016 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.7 84: (ns/day) (hour/ns) 84: Performance: 1757.157 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.5 84: (ns/day) (hour/ns) 84: Performance: 1911.447 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.9 84: (ns/day) (hour/ns) 84: Performance: 1349.823 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1783.095 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1786.197 0.013 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (29 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1381.609 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.1 84: (ns/day) (hour/ns) 84: Performance: 1209.145 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.4 84: (ns/day) (hour/ns) 84: Performance: 1698.069 0.014 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1638.456 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1626.774 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1184.730 0.020 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (30 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1129.970 0.021 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1273.903 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1050.400 0.023 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1282.388 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1288.827 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.1 84: (ns/day) (hour/ns) 84: Performance: 1068.991 0.022 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (32 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1331.732 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1489.505 0.016 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1355.764 0.018 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 97.0 84: (ns/day) (hour/ns) 84: Performance: 1506.995 0.016 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.9 84: (ns/day) (hour/ns) 84: Performance: 1593.532 0.015 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 96.8 84: (ns/day) (hour/ns) 84: Performance: 1231.626 0.019 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (31 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (985 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (997 ms total) 84: [ PASSED ] 25 tests. 84/92 Test #84: MdrunCoordinationCouplingTests1Rank ....... Passed 1.02 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 195.5 85: (ns/day) (hour/ns) 85: Performance: 771.376 0.031 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.4 85: (ns/day) (hour/ns) 85: Performance: 1749.423 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.4%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1926.088 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1793.738 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 98.4%. 85: The balanceable part of the MD step is 29%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 28.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 28.3 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.114 0.057 199.8 85: (ns/day) (hour/ns) 85: Performance: 25.728 0.933 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 35%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1889.463 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (336 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.2 85: (ns/day) (hour/ns) 85: Performance: 1413.791 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.7 85: (ns/day) (hour/ns) 85: Performance: 1566.385 0.015 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 19.9%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 10.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 10.9 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 17 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.632 0.840 194.3 85: (ns/day) (hour/ns) 85: Performance: 1.749 13.725 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1597.457 0.015 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1753.656 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.4%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.4%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1745.211 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2202 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1415.252 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1626.989 0.015 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.9%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 1691.077 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 18.7%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 9.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 9.5 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 15 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.216 0.624 194.9 85: (ns/day) (hour/ns) 85: Performance: 2.354 10.196 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.3%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1760.924 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.1%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1855.880 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1563 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 25 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.6 85: (ns/day) (hour/ns) 85: Performance: 1441.243 0.017 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1711.752 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.0%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1910.262 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1889.463 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1825.091 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.3%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.4%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1797.139 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (533 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1626.989 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1875.942 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2037.907 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.320 0.690 191.3 85: (ns/day) (hour/ns) 85: Performance: 2.129 11.274 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.212 0.638 190.0 85: (ns/day) (hour/ns) 85: Performance: 2.302 10.424 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 2082.689 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3342 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 40 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.270 0.135 199.9 85: (ns/day) (hour/ns) 85: Performance: 10.881 2.206 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1807.421 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2132.431 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 53 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.376 0.704 195.5 85: (ns/day) (hour/ns) 85: Performance: 2.087 11.502 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1982.811 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.512 0.780 193.9 85: (ns/day) (hour/ns) 85: Performance: 1.883 12.745 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4584 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.529 0.765 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.921 12.494 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1802.397 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 2023.516 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 1962.285 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.5 85: (ns/day) (hour/ns) 85: Performance: 1937.598 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1962.285 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1555 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1558.657 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1852.532 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 2137.240 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.5 85: (ns/day) (hour/ns) 85: Performance: 1981.217 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 187.8 85: (ns/day) (hour/ns) 85: Performance: 1936.685 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1954.503 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (263 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.3 85: (ns/day) (hour/ns) 85: Performance: 1643.263 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.7 85: (ns/day) (hour/ns) 85: Performance: 1904.651 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2204.148 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2079.525 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 2129.483 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 2146.174 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (267 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.8 85: (ns/day) (hour/ns) 85: Performance: 1585.738 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 1882.822 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.7 85: (ns/day) (hour/ns) 85: Performance: 2130.956 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 2002.143 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 1968.555 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1989.213 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (283 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.700 0.874 194.5 85: (ns/day) (hour/ns) 85: Performance: 1.681 14.279 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1852.253 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 2045.010 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 2003.771 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1931.221 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 2072.529 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2013 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.748 0.898 194.7 85: (ns/day) (hour/ns) 85: Performance: 1.636 14.672 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1880.810 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.2 85: (ns/day) (hour/ns) 85: Performance: 2143.561 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 2069.049 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1978.671 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 33 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 188.4 85: (ns/day) (hour/ns) 85: Performance: 1877.944 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2587 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.4 85: (ns/day) (hour/ns) 85: Performance: 1641.949 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.7 85: (ns/day) (hour/ns) 85: Performance: 1729.775 0.014 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 29 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2235.339 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 2123.244 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 2107.627 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.3 85: (ns/day) (hour/ns) 85: Performance: 2093.304 0.011 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (894 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.136 0.584 194.5 85: (ns/day) (hour/ns) 85: Performance: 2.515 9.542 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.9 85: (ns/day) (hour/ns) 85: Performance: 1866.847 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.408 0.728 193.4 85: (ns/day) (hour/ns) 85: Performance: 2.018 11.894 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.237 0.619 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.375 10.107 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 2058.678 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.6 85: (ns/day) (hour/ns) 85: Performance: 2056.616 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (4727 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 27 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 192.0 85: (ns/day) (hour/ns) 85: Performance: 1646.997 0.015 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 28 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1876.513 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 2057.303 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.6 85: (ns/day) (hour/ns) 85: Performance: 2004.097 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 55 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.508 0.780 193.3 85: (ns/day) (hour/ns) 85: Performance: 1.883 12.744 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.905 0.453 200.0 85: (ns/day) (hour/ns) 85: Performance: 3.245 7.396 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3276 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.576 0.804 196.0 85: (ns/day) (hour/ns) 85: Performance: 1.827 13.136 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 59 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.388 0.718 193.3 85: (ns/day) (hour/ns) 85: Performance: 2.046 11.731 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 59 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.368 0.710 192.7 85: (ns/day) (hour/ns) 85: Performance: 2.069 11.600 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.7 85: (ns/day) (hour/ns) 85: Performance: 1885.992 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 34 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.001 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 2000.193 0.012 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 55 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.572 0.814 193.1 85: (ns/day) (hour/ns) 85: Performance: 1.804 13.301 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (7211 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 59%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 191.2 85: (ns/day) (hour/ns) 85: Performance: 1104.940 0.022 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.0%. 85: The balanceable part of the MD step is 69%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 53 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.120 1.584 197.0 85: (ns/day) (hour/ns) 85: Performance: 0.927 25.880 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.1%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1402.845 0.017 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 39.7%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 15.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 15.7 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 13 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 22 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.172 1.110 195.7 85: (ns/day) (hour/ns) 85: Performance: 1.323 18.135 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.7%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.0 85: (ns/day) (hour/ns) 85: Performance: 1263.323 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.2%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.4%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1254.959 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (4401 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.0%. 85: The balanceable part of the MD step is 62%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.1%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.1 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 40 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.986 0.993 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.479 16.225 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1121.535 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1143.816 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.9 85: (ns/day) (hour/ns) 85: Performance: 1137.690 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.2%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1143.179 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.5%. 85: The balanceable part of the MD step is 67%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.7 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.694 1.347 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.091 22.007 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3335 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.519 0.259 200.0 85: (ns/day) (hour/ns) 85: Performance: 5.662 4.239 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.8%. 85: The balanceable part of the MD step is 68%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 8.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.512 1.280 196.3 85: (ns/day) (hour/ns) 85: Performance: 1.148 20.914 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.7%. 85: The balanceable part of the MD step is 67%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.9 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 57 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.040 1.546 196.6 85: (ns/day) (hour/ns) 85: Performance: 0.950 25.261 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.4%. 85: The balanceable part of the MD step is 65%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.556 1.294 197.5 85: (ns/day) (hour/ns) 85: Performance: 1.135 21.141 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.3 85: (ns/day) (hour/ns) 85: Performance: 1254.576 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.610 0.305 200.0 85: (ns/day) (hour/ns) 85: Performance: 4.813 4.987 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (7472 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 7 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.2 85: (ns/day) (hour/ns) 85: Performance: 1050.221 0.023 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1225.135 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1353.977 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.8 85: (ns/day) (hour/ns) 85: Performance: 1144.241 0.021 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.8 85: (ns/day) (hour/ns) 85: Performance: 1320.174 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1312.860 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (222 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 190.5 85: (ns/day) (hour/ns) 85: Performance: 1054.535 0.023 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1215.347 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1365.682 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 54 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.980 1.514 196.9 85: (ns/day) (hour/ns) 85: Performance: 0.970 24.736 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.178 0.089 199.8 85: (ns/day) (hour/ns) 85: Performance: 16.459 1.458 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1249.867 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (3026 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.5 85: (ns/day) (hour/ns) 85: Performance: 1124.606 0.021 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1228.924 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 6 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.1 85: (ns/day) (hour/ns) 85: Performance: 1345.548 0.018 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 58 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.492 1.290 193.2 85: (ns/day) (hour/ns) 85: Performance: 1.139 21.076 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 187.9 85: (ns/day) (hour/ns) 85: Performance: 1255.726 0.019 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.0 85: (ns/day) (hour/ns) 85: Performance: 1229.782 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (2275 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.232 1.632 198.1 85: (ns/day) (hour/ns) 85: Performance: 0.900 26.664 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.1 85: (ns/day) (hour/ns) 85: Performance: 1051.386 0.023 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1188.730 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.254 0.127 199.9 85: (ns/day) (hour/ns) 85: Performance: 11.552 2.078 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 189.1 85: (ns/day) (hour/ns) 85: Performance: 1185.071 0.020 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.6 85: (ns/day) (hour/ns) 85: Performance: 1109.217 0.022 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (3050 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.6 85: (ns/day) (hour/ns) 85: Performance: 832.963 0.029 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 190.5 85: (ns/day) (hour/ns) 85: Performance: 896.478 0.027 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.002 189.1 85: (ns/day) (hour/ns) 85: Performance: 952.105 0.025 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 993.164 0.024 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 189.4 85: (ns/day) (hour/ns) 85: Performance: 997.829 0.024 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 17 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.029 0.515 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.854 8.409 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1254 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 51 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.220 1.636 196.8 85: (ns/day) (hour/ns) 85: Performance: 0.898 26.729 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 53 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.428 1.240 195.8 85: (ns/day) (hour/ns) 85: Performance: 1.185 20.258 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 61 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.664 1.362 195.6 85: (ns/day) (hour/ns) 85: Performance: 1.078 22.253 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1073.274 0.022 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 189.0 85: (ns/day) (hour/ns) 85: Performance: 1096.094 0.022 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 5 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.003 0.001 188.3 85: (ns/day) (hour/ns) 85: Performance: 1104.049 0.022 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (6269 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (66954 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (66966 ms total) 85: [ PASSED ] 25 tests. 85/92 Test #85: MdrunCoordinationCouplingTests2Ranks ...... Passed 67.00 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1626.345 0.015 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 90 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.6 86: (ns/day) (hour/ns) 86: Performance: 162.142 0.148 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2204.148 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 1939.123 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.1 86: (ns/day) (hour/ns) 86: Performance: 288.121 0.083 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.5 86: (ns/day) (hour/ns) 86: Performance: 163.754 0.147 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3709 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.0 86: (ns/day) (hour/ns) 86: Performance: 278.307 0.086 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 1817.821 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2125.809 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2133.170 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 1917.396 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2005.402 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3273 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.004 0.004 98.8 86: (ns/day) (hour/ns) 86: Performance: 399.364 0.060 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 1879.949 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 20 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1756.656 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2044.671 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2043.315 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 1919.188 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3737 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.5 86: (ns/day) (hour/ns) 86: Performance: 184.460 0.130 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2006.708 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2331.792 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 1973.917 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 92.9 86: (ns/day) (hour/ns) 86: Performance: 1980.262 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2063.159 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4028 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.6 86: (ns/day) (hour/ns) 86: Performance: 114.898 0.209 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1223.311 0.020 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 1582.480 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2021.856 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2029.850 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 1952.026 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3063 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.4 86: (ns/day) (hour/ns) 86: Performance: 180.800 0.133 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1899.659 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2108.348 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2050.797 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2208.098 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2226.452 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4010 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 98.2 86: (ns/day) (hour/ns) 86: Performance: 759.161 0.032 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1800.817 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 2043.993 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1644.579 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 2002.794 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1663.676 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2502 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 1583.700 0.015 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 97.8 86: (ns/day) (hour/ns) 86: Performance: 951.002 0.025 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2051.480 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2050.797 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 1955.123 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1967.612 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2958 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.5 86: (ns/day) (hour/ns) 86: Performance: 181.755 0.132 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1822.661 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 2079.174 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1596.836 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 1910.854 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1890.913 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3067 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.005 0.005 99.3 86: (ns/day) (hour/ns) 86: Performance: 282.402 0.085 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1405.566 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1699.943 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1629.787 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1332.308 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1546.722 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2773 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.003 0.003 98.7 86: (ns/day) (hour/ns) 86: Performance: 515.229 0.047 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 88 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.6 86: (ns/day) (hour/ns) 86: Performance: 158.623 0.151 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.6 86: (ns/day) (hour/ns) 86: Performance: 158.860 0.151 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1535.542 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1502.217 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1452.628 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (4382 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.1 86: (ns/day) (hour/ns) 86: Performance: 1381.919 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1570.378 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1648.540 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.5 86: (ns/day) (hour/ns) 86: Performance: 159.217 0.151 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.5 86: (ns/day) (hour/ns) 86: Performance: 159.617 0.150 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1567.980 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3930 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.6 86: (ns/day) (hour/ns) 86: Performance: 118.850 0.202 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1421.457 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1480.912 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1430.036 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 1525.277 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1316.648 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3444 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (44881 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (44897 ms total) 86: [ PASSED ] 13 tests. 86/92 Test #86: MdrunCoordinationConstraintsTests1Rank .... Passed 44.93 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 24 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 192.7 87: (ns/day) (hour/ns) 87: Performance: 1286.136 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 15 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.988 1.018 195.3 87: (ns/day) (hour/ns) 87: Performance: 1.443 16.633 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.1%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.1%. 87: 87: 87: NOTE: 19 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.220 0.626 194.9 87: (ns/day) (hour/ns) 87: Performance: 2.347 10.228 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1785.679 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.0%. 87: The balanceable part of the MD step is 34%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1716.760 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 35%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1547.499 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7442 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 24 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.6 87: (ns/day) (hour/ns) 87: Performance: 1186.441 0.020 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 24 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1571.580 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1779.490 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1485.554 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 14 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.180 1.114 195.7 87: (ns/day) (hour/ns) 87: Performance: 1.319 18.202 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1662.554 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (6646 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 24 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.4 87: (ns/day) (hour/ns) 87: Performance: 1247.210 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 14 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.004 1.026 195.3 87: (ns/day) (hour/ns) 87: Performance: 1.432 16.764 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 5 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1761.932 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1583.090 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.0%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.0%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.566 0.283 200.0 87: (ns/day) (hour/ns) 87: Performance: 5.191 4.623 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1718.916 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (7345 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.031 0.016 199.0 87: (ns/day) (hour/ns) 87: Performance: 93.583 0.256 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.4 87: (ns/day) (hour/ns) 87: Performance: 1730.990 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 16 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.646 0.323 200.0 87: (ns/day) (hour/ns) 87: Performance: 4.550 5.275 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1707.245 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1681.385 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.048 1.050 195.1 87: (ns/day) (hour/ns) 87: Performance: 1.399 17.156 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6760 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.005 0.003 195.9 87: (ns/day) (hour/ns) 87: Performance: 535.262 0.045 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1574.995 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 1811.939 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1779.747 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.0 87: (ns/day) (hour/ns) 87: Performance: 1717.239 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1721.077 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4885 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 197.7 87: (ns/day) (hour/ns) 87: Performance: 302.829 0.079 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1536.883 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.360 1.210 195.1 87: (ns/day) (hour/ns) 87: Performance: 1.214 19.771 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1748.430 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 3.008 1.552 193.8 87: (ns/day) (hour/ns) 87: Performance: 0.946 25.359 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1656.964 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (8332 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.039 0.020 199.3 87: (ns/day) (hour/ns) 87: Performance: 75.021 0.320 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.256 1.158 194.8 87: (ns/day) (hour/ns) 87: Performance: 1.268 18.921 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.5 87: (ns/day) (hour/ns) 87: Performance: 1698.537 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.460 1.256 195.9 87: (ns/day) (hour/ns) 87: Performance: 1.169 20.522 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1745.211 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1792.694 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (8711 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.750 1.375 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.068 22.471 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.3 87: (ns/day) (hour/ns) 87: Performance: 1537.650 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1721.558 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.8 87: (ns/day) (hour/ns) 87: Performance: 1638.892 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1520.008 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1536.116 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (7721 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 192.5 87: (ns/day) (hour/ns) 87: Performance: 1192.642 0.020 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1468.906 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent in domain decomposition, 87: 3 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.7 87: (ns/day) (hour/ns) 87: Performance: 1458.992 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1571.580 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1549.250 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.7 87: (ns/day) (hour/ns) 87: Performance: 1619.291 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (6685 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.3%. 87: The balanceable part of the MD step is 60%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 41 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 3.916 1.982 197.6 87: (ns/day) (hour/ns) 87: Performance: 0.741 32.383 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.4%. 87: The balanceable part of the MD step is 59%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.724 1.378 197.7 87: (ns/day) (hour/ns) 87: Performance: 1.066 22.513 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1249.867 0.019 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1126.869 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1156.810 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.1%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.0%. 87: 87: 87: NOTE: 13 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 20 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.348 1.202 195.4 87: (ns/day) (hour/ns) 87: Performance: 1.222 19.639 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (10456 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 58%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 62 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.070 0.035 199.3 87: (ns/day) (hour/ns) 87: Performance: 41.582 0.577 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 24%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 193.6 87: (ns/day) (hour/ns) 87: Performance: 666.659 0.036 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.610 0.305 200.0 87: (ns/day) (hour/ns) 87: Performance: 4.814 4.986 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1113.729 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1125.017 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 51%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 189.9 87: (ns/day) (hour/ns) 87: Performance: 1088.733 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (4288 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.028 0.014 198.7 87: (ns/day) (hour/ns) 87: Performance: 104.421 0.230 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1044.700 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 1178.497 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.8 87: (ns/day) (hour/ns) 87: Performance: 1125.737 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1140.534 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.7 87: (ns/day) (hour/ns) 87: Performance: 1151.728 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (4309 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.006 0.003 193.4 87: (ns/day) (hour/ns) 87: Performance: 515.337 0.047 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 5 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1015.427 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 17 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.234 0.617 200.0 87: (ns/day) (hour/ns) 87: Performance: 2.380 10.082 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 1073.742 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1115.645 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generating 1-4 interactions: fudge = 0.5 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 87: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1101.975 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (4724 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (88307 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (88315 ms total) 87: [ PASSED ] 13 tests. 87/92 Test #87: MdrunCoordinationConstraintsTests2Ranks ... Passed 88.36 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.030 0.015 199.4 88: (ns/day) (hour/ns) 88: Performance: 98.905 0.243 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 88: 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: NOTE: 10 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.131 0.066 199.7 88: (ns/day) (hour/ns) 88: Performance: 11.815 2.031 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (157 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: NOTE: 16 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.042 0.021 199.6 88: (ns/day) (hour/ns) 88: Performance: 8.179 2.934 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (40 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (197 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -809500682 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.838 0.419 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.331 5.541 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 88: 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (567 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -436656665 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.441 0.720 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.518 9.530 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (911 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -16798785 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.694 0.347 200.0 88: (ns/day) (hour/ns) 88: Performance: 5.227 4.591 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (523 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -808748369 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.739 0.369 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.911 4.887 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (419 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -1115686161 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.95 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.879 0.439 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.130 5.812 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (503 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to 2147466979 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 4.755 2.378 200.0 88: (ns/day) (hour/ns) 88: Performance: 3.670 6.539 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (2553 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1644500044 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.158 0.579 200.0 88: (ns/day) (hour/ns) 88: Performance: 3.134 7.657 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (713 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1946124271 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.221 0.610 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.973 8.074 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (815 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -38076530 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.87 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.723 0.362 200.0 88: (ns/day) (hour/ns) 88: Performance: 5.018 4.782 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (539 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.830 0.415 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.369 5.494 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: Setting the LD random seed to -805455533 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.87 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (659 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -1086920273 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.93 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.317 0.659 200.0 88: (ns/day) (hour/ns) 88: Performance: 2.755 8.712 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (887 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1873725948 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.88 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.891 0.445 200.0 88: (ns/day) (hour/ns) 88: Performance: 4.073 5.892 88: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (607 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (9707 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (9932 ms total) 88: [ PASSED ] 14 tests. 88/92 Test #88: MdrunFEPTests ............................. Passed 9.97 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.311 0.155 199.9 89: (ns/day) (hour/ns) 89: Performance: 11.670 2.057 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (694 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 12 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.318 0.159 199.9 89: (ns/day) (hour/ns) 89: Performance: 11.398 2.106 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (811 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.317 0.159 199.9 89: (ns/day) (hour/ns) 89: Performance: 11.424 2.101 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (810 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 16 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.338 0.169 199.9 89: (ns/day) (hour/ns) 89: Performance: 10.737 2.235 89: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (842 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (3159 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (3174 ms total) 89: [ PASSED ] 4 tests. 89/92 Test #89: MdrunPullTests ............................ Passed 3.21 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -780288069 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.260 0.130 199.9 90: (ns/day) (hour/ns) 90: Performance: 34.544 0.695 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (148 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -30689281 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.180 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.947 0.481 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (98 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -83886210 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.181 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.710 0.483 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (98 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1169232098 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.180 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 50.017 0.480 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (98 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -138528365 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 18 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.190 0.095 199.9 90: (ns/day) (hour/ns) 90: Performance: 47.343 0.507 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (103 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 2013255675 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.180 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.799 0.482 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (98 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -3192234 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.180 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.761 0.482 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (99 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -537463474 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 19 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.180 0.090 199.9 90: (ns/day) (hour/ns) 90: Performance: 49.863 0.481 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (98 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1944567254 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 16 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.218 0.109 199.9 90: (ns/day) (hour/ns) 90: Performance: 41.200 0.583 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (117 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -276955427 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 21 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.324 0.162 199.9 90: (ns/day) (hour/ns) 90: Performance: 27.740 0.865 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (178 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1074004514 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 24 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.313 0.156 199.9 90: (ns/day) (hour/ns) 90: Performance: 28.733 0.835 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (170 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -588251649 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 21 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.316 0.158 199.9 90: (ns/day) (hour/ns) 90: Performance: 28.462 0.843 90: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (166 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (1477 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (1489 ms total) 90: [ PASSED ] 12 tests. 90/92 Test #90: MdrunRotationTests ........................ Passed 1.51 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 94 tests from 4 test suites. 91: [----------] Global test environment set-up. 91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 16 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.038 0.019 199.7 91: (ns/day) (hour/ns) 91: Performance: 77.969 0.308 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 11 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.164 0.082 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.910 1.340 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 91: 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (133 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.189 0.095 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.507 1.548 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 10 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.171 0.085 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.214 1.394 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (190 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.130 0.065 199.9 91: (ns/day) (hour/ns) 91: Performance: 22.517 1.066 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.140 0.070 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.916 1.147 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (146 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.135 0.067 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.812 1.100 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.145 0.073 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.213 1.187 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (151 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.135 0.068 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.669 1.108 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.145 0.072 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.284 1.183 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (151 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.132 0.066 199.9 91: (ns/day) (hour/ns) 91: Performance: 22.244 1.079 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.140 0.070 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.896 1.149 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (147 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.135 0.067 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.823 1.100 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.145 0.073 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.244 1.186 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (151 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.135 0.068 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.741 1.104 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.145 0.072 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.281 1.183 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (151 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: MTTK coupling is deprecated and will soon be removed 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.259 0.130 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.332 2.118 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.198 0.099 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.830 1.618 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (240 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.233 0.117 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.589 1.906 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.285 0.142 199.9 91: (ns/day) (hour/ns) 91: Performance: 10.321 2.325 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (289 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.335 0.168 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.769 2.737 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.299 0.149 199.9 91: (ns/day) (hour/ns) 91: Performance: 9.832 2.441 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (351 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 91: MTTK coupling is deprecated and will soon be removed 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.445 0.223 199.9 91: (ns/day) (hour/ns) 91: Performance: 6.596 3.638 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.238 0.119 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.353 1.943 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (356 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.241 0.121 198.8 91: (ns/day) (hour/ns) 91: Performance: 12.123 1.980 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.151 0.076 199.8 91: (ns/day) (hour/ns) 91: Performance: 19.385 1.238 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (215 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.141 0.071 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.778 1.155 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.151 0.076 199.9 91: (ns/day) (hour/ns) 91: Performance: 19.418 1.236 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (157 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.144 0.072 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.389 1.177 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.152 0.076 199.9 91: (ns/day) (hour/ns) 91: Performance: 19.367 1.239 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (158 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.166 0.083 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.708 1.355 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.212 0.106 199.9 91: (ns/day) (hour/ns) 91: Performance: 13.844 1.734 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (200 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.170 0.085 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.290 1.388 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.183 0.091 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.053 1.495 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (187 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Center of mass removal not necessary for Andersen. All velocities of 91: coupled groups are rerandomized periodically, so flying ice cube errors 91: will not occur. 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.171 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.158 1.399 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.181 0.090 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.264 1.476 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (187 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 11 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.262 0.131 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.214 2.140 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 12 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.267 0.133 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.017 2.179 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (810 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 11 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.268 0.134 199.9 91: (ns/day) (hour/ns) 91: Performance: 10.954 2.191 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 14 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.327 0.164 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.969 2.676 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (900 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.248 0.124 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.835 2.028 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.223 0.112 199.9 91: (ns/day) (hour/ns) 91: Performance: 13.157 1.824 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (1108 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.170 0.085 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.291 1.388 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.171 0.085 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.211 1.394 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (516 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.267 0.134 199.9 91: (ns/day) (hour/ns) 91: Performance: 10.988 2.184 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.260 0.130 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.274 2.129 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (930 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.168 0.084 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.497 1.372 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.170 0.085 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.274 1.389 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (778 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.172 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.080 1.405 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.173 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.986 1.413 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (602 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.181 0.091 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.212 1.480 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.173 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.985 1.413 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (543 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.338 0.169 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.693 2.761 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.199 0.100 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.744 1.628 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (994 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.242 0.121 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.124 1.979 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.173 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.997 1.412 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (664 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.337 0.169 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.702 2.758 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.280 0.140 199.9 91: (ns/day) (hour/ns) 91: Performance: 10.488 2.288 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (997 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.184 0.092 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.948 1.505 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.180 0.090 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.281 1.474 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (557 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: Andersen temperature control methods assume nsttcouple = 1; there is no 91: need for larger nsttcouple > 1, since no global parameters are computed. 91: nsttcouple has been reset to 1 91: 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 10 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.212 0.106 199.9 91: (ns/day) (hour/ns) 91: Performance: 13.862 1.731 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.180 0.090 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.335 1.469 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (550 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 91: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 91: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (13529 ms total) 91: 91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 13 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.140 0.070 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.939 1.146 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.191 0.095 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.391 1.559 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (178 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 16 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.186 0.093 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.772 1.522 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 13 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.197 0.098 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.936 1.607 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (211 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 91: NVE simulation: will use the initial temperature of 68.810 K for 91: determining the Verlet buffer size 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 18 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.161 0.080 199.9 91: (ns/day) (hour/ns) 91: Performance: 18.272 1.313 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 13 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.130 0.065 199.9 91: (ns/day) (hour/ns) 91: Performance: 22.645 1.060 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (160 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.114 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.828 0.929 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.118 0.059 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.910 0.963 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (127 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.114 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.775 0.931 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.117 0.059 199.9 91: (ns/day) (hour/ns) 91: Performance: 25.019 0.959 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (126 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.177 0.088 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.616 1.444 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 12 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.143 0.071 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.598 1.165 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (174 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.119 0.059 199.8 91: (ns/day) (hour/ns) 91: Performance: 24.712 0.971 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.122 0.061 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.075 0.997 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (131 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.113 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.960 0.925 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.117 0.058 199.9 91: (ns/day) (hour/ns) 91: Performance: 25.167 0.954 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (126 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.114 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.808 0.930 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.117 0.059 199.9 91: (ns/day) (hour/ns) 91: Performance: 25.049 0.958 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (126 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.120 0.060 199.8 91: (ns/day) (hour/ns) 91: Performance: 24.446 0.982 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.121 0.061 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.213 0.991 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (131 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 2 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.118 0.059 199.8 91: (ns/day) (hour/ns) 91: Performance: 24.907 0.964 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.121 0.060 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.294 0.988 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (130 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.114 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.713 0.933 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.117 0.059 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.104 0.956 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (127 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.113 0.057 199.8 91: (ns/day) (hour/ns) 91: Performance: 25.891 0.927 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.117 0.059 199.9 91: (ns/day) (hour/ns) 91: Performance: 25.085 0.957 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (126 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.118 0.059 199.8 91: (ns/day) (hour/ns) 91: Performance: 24.910 0.963 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.121 0.061 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.246 0.990 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (131 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Number of degrees of freedom in T-Coupling group System is 33.00 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: Generated 1 of the 1 non-bonded parameter combinations 91: 91: Excluding 1 bonded neighbours molecule type 'Argon' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.118 0.059 199.8 91: (ns/day) (hour/ns) 91: Performance: 24.825 0.967 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'Argon' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.121 0.061 199.9 91: (ns/day) (hour/ns) 91: Performance: 24.244 0.990 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (130 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.184 0.092 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.978 1.502 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 12 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.142 0.071 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.719 1.158 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (508 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 17 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.194 0.097 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.099 1.590 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 12 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.141 0.071 199.9 91: (ns/day) (hour/ns) 91: Performance: 20.773 1.155 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (469 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: NVE simulation: will use the initial temperature of 398.997 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 12 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.151 0.076 199.8 91: (ns/day) (hour/ns) 91: Performance: 19.447 1.234 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.197 0.099 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.896 1.611 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (457 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.144 0.072 199.8 91: (ns/day) (hour/ns) 91: Performance: 20.407 1.176 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.133 0.067 199.9 91: (ns/day) (hour/ns) 91: Performance: 22.010 1.090 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (542 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 10 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.254 0.127 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.572 2.074 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.149 0.075 199.9 91: (ns/day) (hour/ns) 91: Performance: 19.643 1.222 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (693 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.132 0.066 199.8 91: (ns/day) (hour/ns) 91: Performance: 22.271 1.078 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.137 0.068 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.447 1.119 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (482 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.195 0.098 199.9 91: (ns/day) (hour/ns) 91: Performance: 15.061 1.594 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.237 0.118 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.415 1.933 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (503 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.204 0.102 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.409 1.666 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.205 0.102 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.354 1.672 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (813 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.134 0.067 199.8 91: (ns/day) (hour/ns) 91: Performance: 21.958 1.093 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.133 0.066 199.8 91: (ns/day) (hour/ns) 91: Performance: 22.099 1.086 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (471 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: 91: WARNING 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There were 2 WARNINGs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.211 0.105 199.9 91: (ns/day) (hour/ns) 91: Performance: 13.924 1.724 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.228 0.114 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.866 1.865 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (827 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: The Berendsen thermostat does not generate the correct kinetic energy 91: distribution, and should not be used for new production simulations (in 91: our opinion). We would recommend the V-rescale thermostat. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 3 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.238 0.119 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.325 1.947 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.205 0.102 199.9 91: (ns/day) (hour/ns) 91: Performance: 14.332 1.675 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (886 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.159 0.079 199.9 91: (ns/day) (hour/ns) 91: Performance: 18.504 1.297 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.132 0.066 199.9 91: (ns/day) (hour/ns) 91: Performance: 22.200 1.081 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (783 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.132 0.066 199.8 91: (ns/day) (hour/ns) 91: Performance: 22.154 1.083 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.133 0.067 199.8 91: (ns/day) (hour/ns) 91: Performance: 22.085 1.087 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (420 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: 91: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: The Berendsen barostat does not generate any strictly correct ensemble, 91: and should not be used for new production simulations (in our opinion). 91: We recommend using the C-rescale barostat instead. 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: 91: There was 1 WARNING 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.182 0.091 199.9 91: (ns/day) (hour/ns) 91: Performance: 16.089 1.492 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.137 0.069 199.9 91: (ns/day) (hour/ns) 91: Performance: 21.362 1.123 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (658 ms) 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 91: 1 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Number of degrees of freedom in T-Coupling group System is 27.00 91: 91: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 91: You are using a plain Coulomb cut-off, which might produce artifacts. 91: You might want to consider using PME electrostatics. 91: 91: 91: 91: There were 4 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.166 0.083 199.8 91: (ns/day) (hour/ns) 91: Performance: 17.703 1.356 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 91: 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.172 0.086 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.119 1.402 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (480 ms) 91: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (11142 ms total) 91: 91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'FirstWaterMolecule' has 3 atoms 91: Pull group 2 'SecondWaterMolecule' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 9.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 2573.591 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 1.112 nm 1.000 nm 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 3 of the 3 non-bonded parameter combinations 91: 91: Generated 3 of the 3 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 13 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.322 0.161 199.9 91: (ns/day) (hour/ns) 91: Performance: 9.108 2.635 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.331 0.165 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.882 2.702 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (357 ms) 91: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (357 ms total) 91: 91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 91: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 91: that with the Verlet scheme, nstlist has no effect on the accuracy of 91: your simulation. 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: Setting nstcalcenergy (100) equal to nstenergy (4) 91: 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'FirstWaterMolecule' has 3 atoms 91: Pull group 2 'SecondWaterMolecule' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 9.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 2573.591 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 1.112 nm 1.000 nm 91: 91: There were 3 NOTEs 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: Generated 3 of the 3 non-bonded parameter combinations 91: 91: Generated 3 of the 3 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.246 0.123 199.9 91: (ns/day) (hour/ns) 91: Performance: 11.914 2.014 91: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI thread 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 16 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: NOTE: 17 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.228 0.114 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.898 1.861 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 91: Opened /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 91: 91: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (269 ms) 91: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (269 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 94 tests from 4 test suites ran. (25343 ms total) 91: [ PASSED ] 94 tests. 91/92 Test #91: MdrunSimulatorComparison .................. Passed 25.38 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /build/reproducible-path/gromacs-2025.1/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 21.4%. 92: The balanceable part of the MD step is 35%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 7.4%. 92: 92: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 92: in the domain decomposition. 92: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 92: You can also consider manually changing the decomposition (option -dd); 92: e.g. by using fewer domains along the box dimension in which there is 92: considerable inhomogeneity in the simulated system. 92: 92: NOTE: 27 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 9 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 2.064 1.068 193.3 92: (ns/day) (hour/ns) 92: Performance: 0.728 32.961 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: trr version: GMX_trn_file (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (2146 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 2.5%. 92: The balanceable part of the MD step is 37%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.9%. 92: 92: 92: NOTE: 34 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 191.8 92: (ns/day) (hour/ns) 92: Performance: 626.126 0.038 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (81 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 2.4%. 92: The balanceable part of the MD step is 38%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.9%. 92: 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.2 92: (ns/day) (hour/ns) 92: Performance: 880.413 0.027 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (115 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.1 92: (ns/day) (hour/ns) 92: Performance: 933.054 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (89 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.2 92: (ns/day) (hour/ns) 92: Performance: 909.000 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (569 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.272 0.660 192.7 92: (ns/day) (hour/ns) 92: Performance: 1.178 20.369 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (1724 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.268 0.658 192.7 92: (ns/day) (hour/ns) 92: Performance: 1.182 20.305 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (1724 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.268 0.662 191.6 92: (ns/day) (hour/ns) 92: Performance: 1.175 20.429 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (1588 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.7 92: (ns/day) (hour/ns) 92: Performance: 960.109 0.025 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (211 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 2.5%. 92: The balanceable part of the MD step is 38%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.0%. 92: 92: 92: NOTE: 27 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 190.5 92: (ns/day) (hour/ns) 92: Performance: 879.582 0.027 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (336 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 2.3%. 92: The balanceable part of the MD step is 43%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.0%. 92: 92: 92: NOTE: 27 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.8 92: (ns/day) (hour/ns) 92: Performance: 909.760 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (83 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.4 92: (ns/day) (hour/ns) 92: Performance: 977.372 0.025 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (43 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.2 92: (ns/day) (hour/ns) 92: Performance: 882.080 0.027 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (63 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 190.4 92: (ns/day) (hour/ns) 92: Performance: 915.121 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (39 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 188.9 92: (ns/day) (hour/ns) 92: Performance: 872.290 0.028 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (170 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 190.1 92: (ns/day) (hour/ns) 92: Performance: 921.195 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (51 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 11 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 10 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.128 0.588 191.8 92: (ns/day) (hour/ns) 92: Performance: 1.323 18.147 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (1345 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.5 92: (ns/day) (hour/ns) 92: Performance: 977.519 0.025 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (34 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 22 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 11 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.929 0.465 200.0 92: (ns/day) (hour/ns) 92: Performance: 1.673 14.342 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (1444 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 29 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.5 92: (ns/day) (hour/ns) 92: Performance: 936.403 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (75 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.002 0.001 189.5 92: (ns/day) (hour/ns) 92: Performance: 915.121 0.026 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: Reading file /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (double precision) 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (88 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (12031 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (12047 ms total) 92: [ PASSED ] 37 tests. 92/92 Test #92: MdrunVirtualSiteTests ..................... Passed 12.07 sec 100% tests passed, 0 tests failed out of 92 Label Time Summary: GTest = 855.39 sec*proc (90 tests) IntegrationTest = 471.78 sec*proc (29 tests) MpiTest = 651.56 sec*proc (21 tests) QuickGpuTest = 159.97 sec*proc (23 tests) SlowGpuTest = 670.76 sec*proc (14 tests) SlowTest = 372.20 sec*proc (14 tests) UnitTest = 11.41 sec*proc (47 tests) Total Test time (real) = 400.29 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/mpi/lib /usr/bin/make -j12 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_array.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 2%] Built target thread_mpi /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc2.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvaratoms.cpp [ 4%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_apath.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_coordnums.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 8%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed 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gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi.so.10 -o ../../lib/libgromacs_mpi.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi.so.10.0.0 ../../lib/libgromacs_mpi.so.10 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi 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/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include 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CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmx cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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-fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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/build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi.so.0 -o ../../lib/libgmxapi_mpi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi.so.0.4.0 ../../lib/libgmxapi_mpi.so.0 ../../lib/libgmxapi_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/launch_0_2_1.cpp /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory 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CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp/sessionresources.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -c 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-Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_resources.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_resources.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_resources.a CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_resources.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp/nullpotential.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_test.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmxapi_extension_test cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_ensemblepotential.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_ensemblepotential.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_ensemblepotential.a CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_ensemblepotential.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmxapi_extension_ensemblepotential cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi/src/cpp/mpi_gromacs_support.cpp /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/mpicxx -DGMX_DOUBLE=0 -Dgmxapi_extension_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -MF CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o.d -o CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file=CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-313-aarch64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o ../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi/lib cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi && /usr/bin/strip /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/gmxapi_staging/gmxapi/_gmxapi.cpython-313-aarch64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target _gmxapi /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file=CMakeFiles/gmxapi_extension.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../lib/myplugin.cpython-313-aarch64-linux-gnu.so CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o ../../../../lib/libgmxapi_extension_ensemblepotential.a ../../../../lib/libgmxapi_extension_test.a ../../../../lib/libgmxapi_extension_resources.a ../../../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi/lib cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/strip /build/reproducible-path/gromacs-2025.1/build/mpi/lib/myplugin.cpython-313-aarch64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target gmxapi_extension cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection 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make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c 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src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_float.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/src/atomic.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc 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src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o 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-DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target thread_mpi /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/rle.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abf.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_abmd.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/options.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT 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/usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_restraint.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 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/build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/findallgputasks.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/reportgpuusage.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 4%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/printtime.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include 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-Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi_d.so.10 -o ../../lib/libgromacs_mpi_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.10.0.0 ../../lib/libgromacs_mpi_d.so.10 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs 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-DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/resourceassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/src 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CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi_d.so.0.4.0 ../../lib/libgmxapi_mpi_d.so.0 ../../lib/libgmxapi_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/samples/argon-forces-integration.cpp /usr/bin/make -f 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CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/mpi/lib /usr/bin/make -j12 -C build/mpi tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -P 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/build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr 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/build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 1%] Built target gmx_objlib [ 1%] Built target scanner [ 1%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend [ 1%] Built target internal_rpc_xdr make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi 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'/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target lmfit_objlib make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 5%] Built target options make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 8%] Built target colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build [ 8%] Built target energyanalysis make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 8%] Built target mdrun_objlib [ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 8%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 9%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 60%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 60%] Built target gmx make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 60%] Built target gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" [ 61%] Built target nblib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.top /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 61%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend [ 61%] Built target argon-forces-integration make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" [ 61%] Built target methane-water-integration make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build Generating 1-4 interactions: fudge = 0.5 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' Number of degrees of freedom in T-Coupling group rest is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Setting the LD random seed to -1077018647 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' Analysing residue names: There are: 2 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 61%] Built target gmxapi_extension_ensemblepotential [ 61%] Built target gmxapi_extension_spc2_water_box cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 61%] Built target gtest /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/src/gtest_main.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest_main.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest_main.so.1.13.0 -o ../../../../lib/libgtest_main.so.1.13.0 CMakeFiles/gtest_main.dir/src/gtest_main.cc.o ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 61%] Built target gtest_main /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/tests/test_histogram.cpp /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -MF CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o.d -o CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/tests/test_bounding_restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_histogram-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi_extension_histogram-test.dir/link.d "CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o" -o ../../../bin/gmxapi_extension_histogram-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 61%] Built target gmxapi_extension_histogram-test cd 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-MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2025.1/build/mpi 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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-Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 64%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make 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'/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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-MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 64%] Built target plumed_applied_forces-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestdata.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 65%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 66%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 66%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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-MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 66%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make 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-MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 68%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 68%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" 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/usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 69%] Built target mdlib-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 69%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp 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'/build/reproducible-path/gromacs-2025.1/build/mpi' [ 70%] Built target fft-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 70%] Built target awh-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, gmx::LJCombinationRule)': /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/testsystem.cpp:94:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 94 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 72%] Built target hardware-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 73%] Built target nbnxm-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 74%] Built target 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'/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include 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src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 74%] Built target ewald-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 74%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/dofit.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 74%] Built target mdspan-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/normaldistribution.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 74%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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74%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make 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"CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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/usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 77%] Built target random-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 78%] Built target taskassignment-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.1/build/mpi 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"CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 78%] Built target pbcutil-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 78%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 80%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 80%] Built target gmxana-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 80%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/mpicxx -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 81%] Built target topology-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" 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"CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend [ 81%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/checkpoint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 81%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/confio.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 81%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 81%] Built target tool-test-with-leaks /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make 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-Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/selectioncollection.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 84%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/swapcoords.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_math.cpp:182:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 84%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/constantacceleration.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 84%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 85%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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"CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisimtest.cpp [ 86%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include 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-DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 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/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 86%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/tests/simd4_vector_operations.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 88%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 88%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/timecontrol.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 89%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 90%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include 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'/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 92%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 93%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 93%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/box.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include 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-Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp cd 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'/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp 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../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/util/tests 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-I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix 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-DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/gmxcalculator.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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94%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target fileio-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" 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'/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem 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api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target nblib-util-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target nblib-integrator-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/angle.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 94%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests/version.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem 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CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 96%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src 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../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 96%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -isystem 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-I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.1/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api -I/build/reproducible-path/gromacs-2025.1/src/testutils/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/nblib/tests -I/build/reproducible-path/gromacs-2025.1/api/nblib/include -I/build/reproducible-path/gromacs-2025.1/api/nblib -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/mpi/lib \ OMPI_MCA_rmaps_base_oversubscribe=1 \ PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.1/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.1/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.1/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2146941757 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.087 0.044 199.7 1: (ns/day) (hour/ns) 1: Performance: 11.554 2.077 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (217 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -11048993 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 17 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.035 0.017 199.5 1: (ns/day) (hour/ns) 1: Performance: 29.043 0.826 1: [ OK ] GmxApiTest.RunnerBasicMD (197 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -876687617 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.161 0.080 199.9 1: (ns/day) (hour/ns) 1: Performance: 44.067 0.545 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.169 0.084 199.9 1: (ns/day) (hour/ns) 1: Performance: 42.029 0.571 1: [ OK ] GmxApiTest.RunnerReinitialize (332 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -313688646 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 16 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.035 0.018 199.4 1: (ns/day) (hour/ns) 1: Performance: 28.636 0.838 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 19 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.5 1: (ns/day) (hour/ns) 1: Performance: 31.477 0.762 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (219 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -539320329 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 35 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.070 0.035 199.7 1: (ns/day) (hour/ns) 1: Performance: 24.129 0.995 1: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 31 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.4 1: (ns/day) (hour/ns) 1: Performance: 21.323 1.126 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (223 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -1225785865 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (154 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (1345 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (1349 ms total) 1: [ PASSED ] 9 tests. 1/96 Test #1: GmxapiExternalInterfaceTests ................. Passed 1.48 sec test 2 Start 2: GmxapiMpiTests 2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests 2: Test timeout computed to be: 600 2: [==========] Running 13 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 13 tests from GmxApiTest 2: [ RUN ] GmxApiTest.AllContext 2: [ OK ] GmxApiTest.AllContext (10 ms) 2: [ RUN ] GmxApiTest.NullContext 2: [ OK ] GmxApiTest.NullContext (0 ms) 2: [ RUN ] GmxApiTest.MpiWorldContext 2: [ OK ] GmxApiTest.MpiWorldContext (7 ms) 2: [ RUN ] GmxApiTest.MpiSplitContext 2: [ OK ] GmxApiTest.MpiSplitContext (5 ms) 2: Setting the LD random seed to -1921538083 2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 2: Setting the LD random seed to -675906849 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 22 % of the run time was spent in domain decomposition, 2: 0 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 17 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.516 0.129 399.8 2: (ns/day) (hour/ns) 2: Performance: 3.920 6.122 2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (369 ms) 2: [ RUN ] GmxApiTest.RunnerBasicMD 2: Setting the LD random seed to -1354973762 2: Setting the LD random seed to 1996158935 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 23 % of the run time was spent in domain decomposition, 2: 17 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 5 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.116 0.029 398.9 2: (ns/day) (hour/ns) 2: Performance: 17.365 1.382 2: [ OK ] GmxApiTest.RunnerBasicMD (219 ms) 2: [ RUN ] GmxApiTest.RunnerReinitialize 2: Setting the LD random seed to -184746041 2: Setting the LD random seed to -1268274210 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: Writing final coordinates. 2: 2: Core t (s) Wall t (s) (%) 2: Time: 1.892 0.473 399.9 2: (ns/day) (hour/ns) 2: Performance: 7.493 3.203 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.598 0.150 399.8 2: (ns/day) (hour/ns) 2: Performance: 23.678 1.014 2: [ OK ] GmxApiTest.RunnerReinitialize (822 ms) 2: [ RUN ] GmxApiTest.RunnerChainedMD 2: Setting the LD random seed to -1684048902 2: Setting the LD random seed to -1048993 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 24 % of the run time was spent in domain decomposition, 2: 17 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.117 0.029 399.1 2: (ns/day) (hour/ns) 2: Performance: 17.261 1.390 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Setting nsteps to 4 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Setting nsteps to 4 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 2: 2: Writing final coordinates. 2: 2: NOTE: 25 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.082 0.021 399.0 2: (ns/day) (hour/ns) 2: Performance: 24.658 0.973 2: 2: 2: [ OK ] GmxApiTest.RunnerChainedMD (230 ms) 2: [ RUN ] GmxApiTest.Status 2: [ OK ] GmxApiTest.Status (0 ms) 2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 2: Setting the LD random seed to -285223333 2: Setting the LD random seed to -37880834 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: 2: Dynamic load balancing report: 2: DLB was turned on during the run due to measured imbalance. 2: Average load imbalance: 19.8%. 2: The balanceable part of the MD step is 12%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 2.3%. 2: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 2: 2: 2: NOTE: 43 % of the run time was spent in domain decomposition, 2: 29 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.349 0.087 399.7 2: (ns/day) (hour/ns) 2: Performance: 9.659 2.485 2: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 24.0%. 2: The balanceable part of the MD step is 12%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 2.8%. 2: 2: 2: NOTE: 40 % of the run time was spent in domain decomposition, 2: 28 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.147 0.037 399.3 2: (ns/day) (hour/ns) 2: Performance: 9.180 2.614 2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (316 ms) 2: [ RUN ] GmxApiTest.SystemConstruction 2: Setting the LD random seed to -69209229 2: Setting the LD random seed to -1084624988 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.SystemConstruction (153 ms) 2: [ RUN ] GmxApiTest.SaneVersionComparisons 2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 2: [ RUN ] GmxApiTest.VersionNamed0_1_Features 2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 2: [----------] 13 tests from GmxApiTest (2139 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 13 tests from 1 test suite ran. (2152 ms total) 2: [ PASSED ] 13 tests. 2/96 Test #2: GmxapiMpiTests ............................... Passed 2.87 sec test 3 Start 3: GmxapiInternalInterfaceTests 3: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests 3: Test timeout computed to be: 600 3: [==========] Running 2 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 2 tests from GmxApiTest 3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to -1074071617 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (160 ms) 3: [ RUN ] GmxApiTest.CreateApiWorkflow 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 1733787055 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.CreateApiWorkflow (149 ms) 3: [----------] 2 tests from GmxApiTest (310 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 2 tests from 1 test suite ran. (314 ms total) 3: [ PASSED ] 2 tests. 3/96 Test #3: GmxapiInternalInterfaceTests ................. Passed 0.39 sec test 4 Start 4: GmxapiInternalsMpiTests 4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests 4: Test timeout computed to be: 600 4: [==========] Running 2 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from GmxApiTest 4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 4: Setting the LD random seed to -428159495 4: Setting the LD random seed to -72351846 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (191 ms) 4: [ RUN ] GmxApiTest.CreateApiWorkflow 4: Setting the LD random seed to -1076003201 4: Setting the LD random seed to -143347417 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.CreateApiWorkflow (154 ms) 4: [----------] 2 tests from GmxApiTest (346 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test suite ran. (362 ms total) 4: [ PASSED ] 2 tests. 4/96 Test #4: GmxapiInternalsMpiTests ...................... Passed 0.76 sec test 5 Start 5: NbLibListedForcesTests 5: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/listed_forces/tests 5: Test timeout computed to be: 600 5: [==========] Running 44 tests from 22 test suites. 5: [----------] Global test environment set-up. 5: [----------] 8 tests from NBlibTest 5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 5: [ RUN ] NBlibTest.BondTypesLessThanWorks 5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 5: [ RUN ] NBlibTest.CanSplitListedWork 5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 5: [ RUN ] NBlibTest.ListedForceBuffer 5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 5: [ RUN ] NBlibTest.EndToEndListedComparison 5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 5: [ RUN ] NBlibTest.shiftForcesAreCorrect 5: [ OK ] NBlibTest.shiftForcesAreCorrect (10 ms) 5: [----------] 8 tests from NBlibTest (11 ms total) 5: 5: [----------] 1 test from Kernels 5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 5: [----------] 1 test from Kernels (0 ms total) 5: 5: [----------] 1 test from FourCenter 5: [ RUN ] FourCenter.ListedForcesProperDihedralTest 5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 5: [----------] 1 test from FourCenter (0 ms total) 5: 5: [----------] 7 tests from ThreeCenter 5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 5: [----------] 7 tests from ThreeCenter (0 ms total) 5: 5: [----------] 5 tests from TwoCenter 5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesG96BondTest 5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesCubicBondTest 5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesMorseBondTest 5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesFeneBondTest 5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 5: [----------] 5 tests from TwoCenter (0 ms total) 5: 5: [----------] 5 tests from ListedExampleData 5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceForces 5: [ OK ] ListedExampleData.CanReduceForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceEnergies 5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 5: [----------] 5 tests from ListedExampleData (0 ms total) 5: 5: [----------] 1 test from LinearChainDataFixture 5: [ RUN ] LinearChainDataFixture.Multithreading 5: [ OK ] LinearChainDataFixture.Multithreading (26 ms) 5: [----------] 1 test from LinearChainDataFixture (26 ms total) 5: 5: [----------] 2 tests from ListedShims 5: [ RUN ] ListedShims.ParameterConversion 5: [ OK ] ListedShims.ParameterConversion (0 ms) 5: [ RUN ] ListedShims.GmxToNblibConversion 5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 5: [----------] 2 tests from ListedShims (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 5: 5: [----------] 1 test from ListedTransformations 5: [ RUN ] ListedTransformations.SortInteractionIndices 5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 5: [----------] 1 test from ListedTransformations (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 44 tests from 22 test suites ran. (39 ms total) 5: [ PASSED ] 44 tests. 5/96 Test #5: NbLibListedForcesTests ....................... Passed 0.17 sec test 6 Start 6: NbLibSamplesTestArgon 6: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/argon-forces-integration 6: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples 6: Test timeout computed to be: 1500 6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 6/96 Test #6: NbLibSamplesTestArgon ........................ Passed 0.08 sec test 7 Start 7: NbLibSamplesTestMethaneWater 7: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/methane-water-integration 7: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples 7: Test timeout computed to be: 1500 7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 7: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 7/96 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.11 sec test 8 Start 8: NbLibUtilTests 8: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/util/tests 8: Test timeout computed to be: 30 8: [==========] Running 16 tests from 2 test suites. 8: [----------] Global test environment set-up. 8: [----------] 6 tests from NBlibTest 8: [ RUN ] NBlibTest.isRealValued 8: [ OK ] NBlibTest.isRealValued (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasNan 8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasInf 8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 8: [ RUN ] NBlibTest.generateVelocitySize 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocitySize (0 ms) 8: [ RUN ] NBlibTest.generateVelocityCheckNumbers 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 8: [----------] 6 tests from NBlibTest (0 ms total) 8: 8: [----------] 10 tests from NblibTraitsUtils 8: [ RUN ] NblibTraitsUtils.FuseTwo 8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 8: [ RUN ] NblibTraitsUtils.Fuse 8: [ OK ] NblibTraitsUtils.Fuse (0 ms) 8: [ RUN ] NblibTraitsUtils.Repeat 8: [ OK ] NblibTraitsUtils.Repeat (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 8: [ RUN ] NblibTraitsUtils.Contains 8: [ OK ] NblibTraitsUtils.Contains (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 8: [----------] 10 tests from NblibTraitsUtils (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 16 tests from 2 test suites ran. (0 ms total) 8: [ PASSED ] 16 tests. 8/96 Test #8: NbLibUtilTests ............................... Passed 0.31 sec test 9 Start 9: NbLibSetupTests 9: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 57 tests from 3 test suites. 9: [----------] Global test environment set-up. 9: [----------] 41 tests from NBlibTest 9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.CubicBoxWorks 9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 9: [ RUN ] NBlibTest.BoxEqual 9: [ OK ] NBlibTest.BoxEqual (0 ms) 9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 9: [ RUN ] NBlibTest.CanMergeInteractions 9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.PbcHolderWorks 9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 9: [ RUN ] NBlibTest.AtWorks 9: [ OK ] NBlibTest.AtWorks (0 ms) 9: [ RUN ] NBlibTest.AtThrows 9: [ OK ] NBlibTest.AtThrows (0 ms) 9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 9: [ RUN ] NBlibTest.CanAddInteractions 9: [ OK ] NBlibTest.CanAddInteractions (0 ms) 9: [ RUN ] NBlibTest.CanAddUreyBradley 9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 9: [ RUN ] NBlibTest.TopologyHasNumParticles 9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 9: [ RUN ] NBlibTest.TopologyHasCharges 9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 9: [ RUN ] NBlibTest.TopologyHasMasses 9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypes 9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 9: [ RUN ] NBlibTest.TopologyHasExclusions 9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 9: [ RUN ] NBlibTest.TopologyHasSequencing 9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 9: [ RUN ] NBlibTest.TopologyCanAggregateBonds 9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 9: [ RUN ] NBlibTest.TopologySequenceIdThrows 9: No particle O-Atom in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractions 9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 9: No particle Iron in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 9: [----------] 41 tests from NBlibTest (1 ms total) 9: 9: [----------] 15 tests from NbnxmSetupTest 9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.updateForcerecWorks 9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 9: [----------] 15 tests from NbnxmSetupTest (0 ms total) 9: 9: [----------] 1 test from VirialsTest 9: [ RUN ] VirialsTest.computeVirialTensorWorks 9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 9: [----------] 1 test from VirialsTest (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 57 tests from 3 test suites ran. (1 ms total) 9: [ PASSED ] 57 tests. 9/96 Test #9: NbLibSetupTests .............................. Passed 0.21 sec test 10 Start 10: NbLibTprTests 10: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibTprTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests 10: Test timeout computed to be: 30 10: [==========] Running 4 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 4 tests from TprReaderTest 10: [ RUN ] TprReaderTest.SimDBTprIsCreated 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.SimDBTprIsCreated (16 ms) 10: [ RUN ] TprReaderTest.Spc2Reads 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Generating 1-4 interactions: fudge = 0.5 10: Number of degrees of freedom in T-Coupling group System is 9.00 10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: NVE simulation: will use the initial temperature of 2573.591 K for 10: determining the Verlet buffer size 10: 10: 10: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: You are using a plain Coulomb cut-off, which might produce artifacts. 10: You might want to consider using PME electrostatics. 10: 10: 10: 10: There were 4 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 10: Generated 3 of the 3 non-bonded parameter combinations 10: 10: Generated 3 of the 3 1-4 parameter combinations 10: 10: Excluding 2 bonded neighbours molecule type 'SOL' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.Spc2Reads (15 ms) 10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (8 ms) 10: [ RUN ] TprReaderTest.FCfromTprDataWorks 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.FCfromTprDataWorks (11 ms) 10: [----------] 4 tests from TprReaderTest (52 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 4 tests from 1 test suite ran. (56 ms total) 10: [ PASSED ] 4 tests. 10/96 Test #10: NbLibTprTests ................................ Passed 0.16 sec test 11 Start 11: NbLibIntegrationTests 11: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests 11: Test timeout computed to be: 600 11: [==========] Running 20 tests from 1 test suite. 11: [----------] Global test environment set-up. 11: [----------] 20 tests from NBlibTest 11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ExpectedNumberOfForces 11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 11: [ RUN ] NBlibTest.CanIntegrateSystem 11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 11: [ RUN ] NBlibTest.UpdateChangesForces 11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.CanConstructSimulationState 11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanMove 11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanAssign 11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasBox 11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 11: [----------] 20 tests from NBlibTest (3 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 20 tests from 1 test suite ran. (3 ms total) 11: [ PASSED ] 20 tests. 11/96 Test #11: NbLibIntegrationTests ........................ Passed 0.11 sec test 12 Start 12: NbLibIntegratorTests 12: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/tests 12: Test timeout computed to be: 600 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from NBlibTest 12: [ RUN ] NBlibTest.IntegratorWorks 12: [ OK ] NBlibTest.IntegratorWorks (0 ms) 12: [----------] 1 test from NBlibTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (0 ms total) 12: [ PASSED ] 1 test. 12/96 Test #12: NbLibIntegratorTests ......................... Passed 0.07 sec test 13 Start 13: TestUtilsUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests 13: Test timeout computed to be: 30 13: [==========] Running 75 tests from 7 test suites. 13: [----------] Global test environment set-up. 13: [----------] 10 tests from InteractiveTestHelperTest 13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 13: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 13: 13: [----------] 10 tests from NameOfTestFromTupleTest 13: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 13: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 13: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 13: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 13: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 13: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 13: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 13: 13: [----------] 3 tests from RefDataFilenameMakerTest 13: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 13: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 13: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 13: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 13: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 13: 13: [----------] 37 tests from ReferenceDataTest 13: [ RUN ] ReferenceDataTest.HandlesSimpleData 13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringBlockData 13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesVectorData 13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceData 13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectData 13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingData 13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedData 13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnys 13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesReadingValues 13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 13: [----------] 37 tests from ReferenceDataTest (2 ms total) 13: 13: [----------] 7 tests from FloatingPointDifferenceTest 13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 13: 13: [----------] 4 tests from FloatingPointToleranceTest 13: [ RUN ] FloatingPointToleranceTest.UlpTolerance 13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 13: 13: [----------] 4 tests from XvgTests 13: [ RUN ] XvgTests.CreateFile 13: [ OK ] XvgTests.CreateFile (0 ms) 13: [ RUN ] XvgTests.CheckMissing 13: [ OK ] XvgTests.CheckMissing (0 ms) 13: [ RUN ] XvgTests.CheckExtra 13: [ OK ] XvgTests.CheckExtra (0 ms) 13: [ RUN ] XvgTests.ReadIncorrect 13: [ OK ] XvgTests.ReadIncorrect (0 ms) 13: [----------] 4 tests from XvgTests (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 75 tests from 7 test suites ran. (4 ms total) 13: [ PASSED ] 75 tests. 13/96 Test #13: TestUtilsUnitTests ........................... Passed 0.08 sec test 14 Start 14: TestUtilsMpiUnitTests 14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/testutils/tests 14: Test timeout computed to be: 30 14: [==========] Running 1 test from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 1 test from MpiSelfTest 14: [ RUN ] MpiSelfTest.Runs 14: [ OK ] MpiSelfTest.Runs (0 ms) 14: [----------] 1 test from MpiSelfTest (0 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 1 test from 1 test suite ran. (0 ms total) 14: [ PASSED ] 1 test. 14/96 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.37 sec test 15 Start 15: UtilityUnitTests 15: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests 15: Test timeout computed to be: 30 15: [==========] Running 420 tests from 65 test suites. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.Move 15: [ OK ] AllocatorTest/0.Move (0 ms) 15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/0.Comparison 15: [ OK ] AllocatorTest/0.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/0 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.Move 15: [ OK ] AllocatorTest/1.Move (0 ms) 15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/1.Comparison 15: [ OK ] AllocatorTest/1.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/1 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.Move 15: [ OK ] AllocatorTest/2.Move (0 ms) 15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/2.Comparison 15: [ OK ] AllocatorTest/2.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/2 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.Move 15: [ OK ] AllocatorTest/3.Move (0 ms) 15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/3.Comparison 15: [ OK ] AllocatorTest/3.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/3 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.Move 15: [ OK ] AllocatorTest/4.Move (0 ms) 15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/4.Comparison 15: [ OK ] AllocatorTest/4.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/4 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.Move 15: [ OK ] AllocatorTest/5.Move (0 ms) 15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/5.Comparison 15: [ OK ] AllocatorTest/5.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/5 (0 ms total) 15: 15: [----------] 1 test from AllocatorUntypedTest 15: [ RUN ] AllocatorUntypedTest.Comparison 15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 15: [----------] 1 test from AllocatorUntypedTest (0 ms total) 15: 15: [----------] 4 tests from EmptyArrayRefTest 15: [ RUN ] EmptyArrayRefTest.IsEmpty 15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 15: 15: [----------] 1 test from EmptyConstArrayRefTest 15: [ RUN ] EmptyConstArrayRefTest.IsEmpty 15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 15: 15: [----------] 8 tests from BoolType 15: [ RUN ] BoolType.ImplicitConversion 15: [ OK ] BoolType.ImplicitConversion (0 ms) 15: [ RUN ] BoolType.FalseByDefault 15: [ OK ] BoolType.FalseByDefault (0 ms) 15: [ RUN ] BoolType.Assignment 15: [ OK ] BoolType.Assignment (0 ms) 15: [ RUN ] BoolType.Copy 15: [ OK ] BoolType.Copy (0 ms) 15: [ RUN ] BoolType.ArrayRefCanBeCreated 15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 15: [ RUN ] BoolType.CanBeCastToBool 15: [ OK ] BoolType.CanBeCastToBool (0 ms) 15: [ RUN ] BoolType.HasSizeOfBool 15: [ OK ] BoolType.HasSizeOfBool (0 ms) 15: [ RUN ] BoolType.HasAlignmentOfBool 15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 15: [----------] 8 tests from BoolType (0 ms total) 15: 15: [----------] 4 tests from ArrayRefFromBoolTypeVector 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.Works 15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 15: 15: [----------] 7 tests from CStringUtilityTest 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 15: [ RUN ] CStringUtilityTest.strip_comment 15: [ OK ] CStringUtilityTest.strip_comment (0 ms) 15: [ RUN ] CStringUtilityTest.upstring 15: [ OK ] CStringUtilityTest.upstring (0 ms) 15: [ RUN ] CStringUtilityTest.ltrim 15: [ OK ] CStringUtilityTest.ltrim (0 ms) 15: [ RUN ] CStringUtilityTest.rtrim 15: [ OK ] CStringUtilityTest.rtrim (0 ms) 15: [ RUN ] CStringUtilityTest.trim 15: [ OK ] CStringUtilityTest.trim (0 ms) 15: [----------] 7 tests from CStringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from DefaultInitializationAllocator 15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 15: 15: [----------] 4 tests from EnumerationHelpersTest 15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 15: 15: [----------] 1 test from EnumClassSuitsEnumerationArray 15: [ RUN ] EnumClassSuitsEnumerationArray.Works 15: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 15: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 15: 15: [----------] 18 tests from FixedCapacityVectorTest 15: [ RUN ] FixedCapacityVectorTest.IsEmpty 15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 15: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PushWorks 15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PopWorks 15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ResizeWorks 15: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ClearWorks 15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.AtThrows 15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 15: [ RUN ] FixedCapacityVectorTest.IteratorWorks 15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 15: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 15: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.DataWorks 15: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 15: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 15: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 15: 15: [----------] 5 tests from InMemorySerializerTest 15: [ RUN ] InMemorySerializerTest.Roundtrip 15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SizeIsCorrect 15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 15: [----------] 5 tests from InMemorySerializerTest (0 ms total) 15: 15: [----------] 4 tests from KeyValueTreeSerializerTest 15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 15: 15: [----------] 7 tests from TreeValueTransformTest 15: [ RUN ] TreeValueTransformTest.SimpleTransforms 15: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromString 15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 15: [ RUN ] TreeValueTransformTest.ScopedTransformRules 15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 15: [----------] 7 tests from TreeValueTransformTest (0 ms total) 15: 15: [----------] 1 test from TreeValueTransformErrorTest 15: [ RUN ] TreeValueTransformErrorTest.ConversionError 15: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 15: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 15: 15: [----------] 9 tests from ListOfLists 15: [ RUN ] ListOfLists.EmptyListOfListsWorks 15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 15: [ RUN ] ListOfLists.AppendWorks 15: [ OK ] ListOfLists.AppendWorks (0 ms) 15: [ RUN ] ListOfLists.EmptyListWorks 15: [ OK ] ListOfLists.EmptyListWorks (0 ms) 15: [ RUN ] ListOfLists.AppendAccessWorks 15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 15: [ RUN ] ListOfLists.ClearWorks 15: [ OK ] ListOfLists.ClearWorks (0 ms) 15: [ RUN ] ListOfLists.OutOfRangeAccessThrows 15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 15: [ RUN ] ListOfLists.FrontAndBackWork 15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 15: [ RUN ] ListOfLists.ExtractsAndRestores 15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 15: [----------] 9 tests from ListOfLists (0 ms total) 15: 15: [----------] 7 tests from LoggerTest 15: [ RUN ] LoggerTest.EmptyLoggerWorks 15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToStream 15: [ OK ] LoggerTest.LogsToStream (0 ms) 15: [ RUN ] LoggerTest.LogsToFile 15: [ OK ] LoggerTest.LogsToFile (0 ms) 15: [ RUN ] LoggerTest.LevelFilteringWorks 15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleStreams 15: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleFiles 15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 15: [ RUN ] LoggerTest.LogsToStreamAndFile 15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 15: [----------] 7 tests from LoggerTest (0 ms total) 15: 15: [----------] 7 tests from MessageStringCollectorTest 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveAssign 15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 15: 15: [----------] 1 test from PathTest 15: [ RUN ] PathTest.StripSourcePrefixWorks 15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 15: [----------] 1 test from PathTest (0 ms total) 15: 15: [----------] 2 tests from PhysicalNodeCommunicatorTest 15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 15: 15: [----------] 5 tests from Range 15: [ RUN ] Range.EmptyRangeWorks 15: [ OK ] Range.EmptyRangeWorks (0 ms) 15: [ RUN ] Range.NonEmptyRangeWorks 15: [ OK ] Range.NonEmptyRangeWorks (0 ms) 15: [ RUN ] Range.BeginEnd 15: [ OK ] Range.BeginEnd (0 ms) 15: [ RUN ] Range.IsInRangeWorks 15: [ OK ] Range.IsInRangeWorks (0 ms) 15: [ RUN ] Range.IteratorWorks 15: [ OK ] Range.IteratorWorks (0 ms) 15: [----------] 5 tests from Range (0 ms total) 15: 15: [----------] 3 tests from ScopeGuardTest 15: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 15: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 15: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 15: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 15: [----------] 3 tests from ScopeGuardTest (0 ms total) 15: 15: [----------] 7 tests from StringConvert 15: [ RUN ] StringConvert.NoResultFromEptyString 15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 15: [ RUN ] StringConvert.ThreeFloatsSuccessfully 15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 15: [ RUN ] StringConvert.OneIntSucessfully 15: [ OK ] StringConvert.OneIntSucessfully (0 ms) 15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 15: [ RUN ] StringConvert.ThrowsWhenWrongSize 15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 15: [----------] 7 tests from StringConvert (0 ms total) 15: 15: [----------] 7 tests from StringToEnumValueConverterTest 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 15: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 15: 15: [----------] 9 tests from StringUtilityTest 15: [ RUN ] StringUtilityTest.StartsWith 15: [ OK ] StringUtilityTest.StartsWith (0 ms) 15: [ RUN ] StringUtilityTest.EndsWith 15: [ OK ] StringUtilityTest.EndsWith (0 ms) 15: [ RUN ] StringUtilityTest.StripSuffixIfPresent 15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 15: [ RUN ] StringUtilityTest.StripString 15: [ OK ] StringUtilityTest.StripString (0 ms) 15: [ RUN ] StringUtilityTest.SplitString 15: [ OK ] StringUtilityTest.SplitString (0 ms) 15: [ RUN ] StringUtilityTest.SplitDelimitedString 15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 15: [----------] 9 tests from StringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from FormatStringTest 15: [ RUN ] FormatStringTest.HandlesBasicFormatting 15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 15: [ RUN ] FormatStringTest.HandlesLongStrings 15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 15: [----------] 2 tests from FormatStringTest (0 ms total) 15: 15: [----------] 1 test from StringFormatterTest 15: [ RUN ] StringFormatterTest.HandlesBasicFormatting 15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 15: [----------] 1 test from StringFormatterTest (0 ms total) 15: 15: [----------] 1 test from formatAndJoinTest 15: [ RUN ] formatAndJoinTest.Works 15: [ OK ] formatAndJoinTest.Works (0 ms) 15: [----------] 1 test from formatAndJoinTest (0 ms total) 15: 15: [----------] 1 test from JoinStringsTest 15: [ RUN ] JoinStringsTest.Works 15: [ OK ] JoinStringsTest.Works (0 ms) 15: [----------] 1 test from JoinStringsTest (0 ms total) 15: 15: [----------] 6 tests from ReplaceAllTest 15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesNoMatches 15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 15: [----------] 6 tests from ReplaceAllTest (0 ms total) 15: 15: [----------] 10 tests from TextLineWrapperTest 15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectly 15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndent 15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 15: [----------] 10 tests from TextLineWrapperTest (0 ms total) 15: 15: [----------] 1 test from CompileTimeStringJoin 15: [ RUN ] CompileTimeStringJoin.Works 15: [ OK ] CompileTimeStringJoin.Works (0 ms) 15: [----------] 1 test from CompileTimeStringJoin (0 ms total) 15: 15: [----------] 3 tests from TemplateMPTest 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 15: [----------] 3 tests from TemplateMPTest (0 ms total) 15: 15: [----------] 6 tests from TextWriterTest 15: [ RUN ] TextWriterTest.WritesLines 15: [ OK ] TextWriterTest.WritesLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInParts 15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 15: [ RUN ] TextWriterTest.WritesWrappedLines 15: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 15: [ RUN ] TextWriterTest.TracksNewlines 15: [ OK ] TextWriterTest.TracksNewlines (0 ms) 15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 15: [----------] 6 tests from TextWriterTest (0 ms total) 15: 15: [----------] 1 test from TypeTraitsTest 15: [ RUN ] TypeTraitsTest.IsIntegralConstant 15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 15: [----------] 1 test from TypeTraitsTest (0 ms total) 15: 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 15: 15: [----------] 11 tests from WithInputPaths/PathSearchTest 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 15: 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 420 tests from 65 test suites ran. (5 ms total) 15: [ PASSED ] 420 tests. 15: 15: YOU HAVE 1 DISABLED TEST 15: 15/96 Test #15: UtilityUnitTests ............................. Passed 0.09 sec test 16 Start 16: UtilityMpiUnitTests 16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/utility/tests 16: Test timeout computed to be: 30 16: [==========] Running 2 tests from 1 test suite. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from PhysicalNodeCommunicatorTest 16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (15 ms) 16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 16: [----------] 2 tests from PhysicalNodeCommunicatorTest (15 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 2 tests from 1 test suite ran. (15 ms total) 16: [ PASSED ] 2 tests. 16/96 Test #16: UtilityMpiUnitTests .......................... Passed 0.23 sec test 17 Start 17: GmxlibTests 17: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxlibTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxlib/nonbonded/tests 17: Test timeout computed to be: 30 17: [==========] Running 78 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 72 tests from NBInteraction/NonbondedFepTest 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (4 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 17: [----------] 72 tests from NBInteraction/NonbondedFepTest (9 ms total) 17: 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 78 tests from 2 test suites ran. (10 ms total) 17: [ PASSED ] 78 tests. 17/96 Test #17: GmxlibTests .................................. Passed 0.33 sec test 18 Start 18: MdlibUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests 18: Test timeout computed to be: 30 18: [==========] Running 1032 tests from 27 test suites. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from EffectiveAtomDensity 18: [ RUN ] EffectiveAtomDensity.VolumeIndependence 18: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 18: [ RUN ] EffectiveAtomDensity.WeightingWorks 18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 18: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 18: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 18: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 18: 18: [----------] 2 tests from AtomNonbondedAndKineticProperties 18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 18: 18: [----------] 1 test from VerletBufferConstraintTest 18: [ RUN ] VerletBufferConstraintTest.EqualMasses 18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 18: 18: [----------] 1 test from VerletBufferSize 18: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 18: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 18: [----------] 1 test from VerletBufferSize (0 ms total) 18: 18: [----------] 6 tests from CalcvirTest 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 18: [----------] 6 tests from CalcvirTest (0 ms total) 18: 18: [----------] 2 tests from PrEbinTest 18: [ RUN ] PrEbinTest.HandlesAverages 18: [ OK ] PrEbinTest.HandlesAverages (0 ms) 18: [ RUN ] PrEbinTest.HandlesEmptyAverages 18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 18: [----------] 2 tests from PrEbinTest (0 ms total) 18: 18: [----------] 3 tests from EnergyDriftTracker 18: [ RUN ] EnergyDriftTracker.emptyWorks 18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.onePointWorks 18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.manyPointsWorks 18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 18: [----------] 3 tests from EnergyDriftTracker (0 ms total) 18: 18: [----------] 4 tests from ShakeTest 18: [ RUN ] ShakeTest.ConstrainsOneBond 18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 18: [----------] 4 tests from ShakeTest (0 ms total) 18: 18: [----------] 1 test from NullSignalTest 18: [ RUN ] NullSignalTest.NullSignallerWorks 18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 18: [----------] 1 test from NullSignalTest (0 ms total) 18: 18: [----------] 7 tests from SignalTest 18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 18: [----------] 7 tests from SignalTest (0 ms total) 18: 18: [----------] 13 tests from UpdateGroupsTest 18: [ RUN ] UpdateGroupsTest.WithEthaneUA 18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 18: [ RUN ] UpdateGroupsTest.WithMethane 18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithEthane 18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFourSite 18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 18: [----------] 13 tests from UpdateGroupsTest (0 ms total) 18: 18: [----------] 1 test from UpdateGroupsCog 18: [ RUN ] UpdateGroupsCog.ComputesCogs 18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 18: [----------] 1 test from UpdateGroupsCog (0 ms total) 18: 18: [----------] 2 tests from WholeMoleculeTransform 18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 18: [ RUN ] WholeMoleculeTransform.HandlesReordering 18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 18: 18: [----------] 28 tests from WithParameters/ConstraintsTest 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (5 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 18: [----------] 28 tests from WithParameters/ConstraintsTest (13 ms total) 18: 18: [----------] 11 tests from WithParameters/EnergyOutputTest 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (3 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 18: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 18: [----------] 11 tests from WithParameters/EnergyOutputTest (14 ms total) 18: 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 18: 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 18: 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 18: 18: [----------] 17 tests from WithParameters/LangevinTest 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 18: [----------] 17 tests from WithParameters/LangevinTest (1 ms total) 18: 18: [----------] 16 tests from WithParameters/LeapFrogTest 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 18: [----------] 16 tests from WithParameters/LeapFrogTest (11 ms total) 18: 18: [----------] 140 tests from Cubic/ParrRahmTest 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Cubic/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from Rectilinear/ParrRahmTest 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Rectilinear/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (4 ms total) 18: 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from TruncOct/ParrRahmTest 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from TruncOct/ParrRahmTest (5 ms total) 18: 18: [----------] 140 tests from Other/ParrRahmTest 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Other/ParrRahmTest (4 ms total) 18: 18: [----------] 13 tests from WithParameters/SettleTest 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 18: [----------] 13 tests from WithParameters/SettleTest (5 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1032 tests from 27 test suites ran. (80 ms total) 18: [ PASSED ] 1032 tests. 18/96 Test #18: MdlibUnitTest ................................ Passed 0.21 sec test 19 Start 19: AwhTest 19: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/AwhTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/awh/tests 19: Test timeout computed to be: 30 19: [==========] Running 25 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from SerializationTest 19: [ RUN ] SerializationTest.CanSerializeDimParams 19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeBiasParams 19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeAwhParams 19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 19: [----------] 3 tests from SerializationTest (0 ms total) 19: 19: [----------] 1 test from BiasTest 19: [ RUN ] BiasTest.DetectsCovering 19: [ OK ] BiasTest.DetectsCovering (0 ms) 19: [----------] 1 test from BiasTest (0 ms total) 19: 19: [----------] 1 test from biasGridTest 19: [ RUN ] biasGridTest.neighborhood 19: [ OK ] biasGridTest.neighborhood (0 ms) 19: [----------] 1 test from biasGridTest (0 ms total) 19: 19: [----------] 2 tests from BiasFepLambdaStateTest 19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 19: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 19: 19: [----------] 8 tests from WithParameters/BiasTest 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 19: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 19: 19: [----------] 2 tests from WithParameters/BiasStateTest 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 19: 19: [----------] 1 test from WithParameters/UserInputTest 19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 19: 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (15 ms total) 19: 19: [----------] 3 tests from WithParameters/FrictionMetricTest 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (10 ms) 19: [----------] 3 tests from WithParameters/FrictionMetricTest (13 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 25 tests from 9 test suites ran. (34 ms total) 19: [ PASSED ] 25 tests. 19/96 Test #19: AwhTest ...................................... Passed 0.22 sec test 20 Start 20: DensityFittingAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/densityfitting/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 2 tests from DensityFittingTest 20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 20: [ RUN ] DensityFittingTest.SingleAtom 20: [ OK ] DensityFittingTest.SingleAtom (0 ms) 20: [----------] 2 tests from DensityFittingTest (0 ms total) 20: 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest 20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 20: 20: [----------] 1 test from DensityFittingForceProviderState 20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 20: 20: [----------] 8 tests from DensityFittingOptionsTest 20: [ RUN ] DensityFittingOptionsTest.DefaultParameters 20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 20: [ RUN ] DensityFittingOptionsTest.KvtToInternal 20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 4 test suites ran. (1 ms total) 20: [ PASSED ] 18 tests. 20/96 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.07 sec test 21 Start 21: QMMMAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests 21: Test timeout computed to be: 30 21: [==========] Running 21 tests from 5 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from QMMMInputGeneratorTest 21: [ RUN ] QMMMInputGeneratorTest.CanConstruct 21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 21: 21: [----------] 7 tests from QMMMTopologyPreprocessorTest 21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -1687552776 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (3 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -1476397125 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -419432457 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -3539201 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (7 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to -301992454 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (7 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 45.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 21: Setting the LD random seed to 1340978615 21: 21: Generated 3 of the 6 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'VSTEST' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 21: 21: Cleaning up constraints and constant bonded interactions with virtual sites 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (3 ms) 21: [----------] 7 tests from QMMMTopologyPreprocessorTest (26 ms total) 21: 21: [----------] 9 tests from QMMMOptionsTest 21: [ RUN ] QMMMOptionsTest.DefaultParameters 21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] QMMMOptionsTest.OptionSetsActive 21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 21: [----------] 9 tests from QMMMOptionsTest (0 ms total) 21: 21: [----------] 1 test from QMMMForceProviderTest 21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 21: [----------] 1 test from QMMMForceProviderTest (0 ms total) 21: 21: [----------] 1 test from QMMMTest 21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from QMMMTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 21 tests from 5 test suites ran. (28 ms total) 21: [ PASSED ] 21 tests. 21/96 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.12 sec test 22 Start 22: ColvarsAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests 22: Test timeout computed to be: 30 22: [==========] Running 16 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 1 test from ColvarsTest 22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 22: [----------] 1 test from ColvarsTest (0 ms total) 22: 22: [----------] 6 tests from ColvarsOptionsTest 22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OptionSetsActive 22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -67110436 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (5 ms) 22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 22: [----------] 6 tests from ColvarsOptionsTest (6 ms total) 22: 22: [----------] 4 tests from ColvarsPreProcessorTest 22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -1879114369 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -201599443 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (3 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -1792147561 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -1342218315 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (3 ms) 22: [----------] 4 tests from ColvarsPreProcessorTest (14 ms total) 22: 22: [----------] 5 tests from ColvarsForceProviderTest 22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 22: [ RUN ] ColvarsForceProviderTest.SimpleInputs 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -1038 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -1094762633 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to 2107013111 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (42 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 66.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: NVE simulation: will use the initial temperature of 300.368 K for 22: determining the Verlet buffer size 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 22: Setting the LD random seed to -4235269 22: 22: Generated 2211 of the 2211 non-bonded parameter combinations 22: 22: Generated 2211 of the 2211 1-4 parameter combinations 22: 22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 22: Analysing residue names: 22: There are: 2 Protein residues 22: Analysing Protein... 22: 22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 22: 22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 22: 22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 22: 22: Note that mdrun will redetermine rlist based on the actual pair-list setup 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (36 ms) 22: [----------] 5 tests from ColvarsForceProviderTest (86 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 16 tests from 4 test suites ran. (107 ms total) 22: [ PASSED ] 16 tests. 22/96 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.25 sec test 23 Start 23: PlumedAppliedForcesUnitTests 23: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests 23: Test timeout computed to be: 30 23: [==========] Running 8 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 8 tests from PlumedOptionsTest 23: [ RUN ] PlumedOptionsTest.defaultConstructor 23: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 23: [ RUN ] PlumedOptionsTest.setTimeStep 23: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 23: [ RUN ] PlumedOptionsTest.setStartingBehavior 23: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 23: [ RUN ] PlumedOptionsTest.setPlumedFile 23: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 23: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 23: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 23: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 23: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 23: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 23: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 23: [ RUN ] PlumedOptionsTest.setTopology 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: 23: NOTE 2 [file angles1.top, line 72]: 23: In moleculetype 'butane' 4 atoms are not bound by a potential or 23: constraint to any other atom in the same moleculetype. Although 23: technically this might not cause issues in a simulation, this often means 23: that the user forgot to add a bond/potential/constraint or put multiple 23: molecules in the same moleculetype definition by mistake. Run with -v to 23: get information for each atom. 23: 23: Number of degrees of freedom in T-Coupling group rest is 9.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 23: NVE simulation: will use the initial temperature of 238.919 K for 23: determining the Verlet buffer size 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Number of degrees of freedom in T-Coupling group rest is 17493.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 23: NVE simulation: will use the initial temperature of 67.983 K for 23: determining the Verlet buffer size 23: 23: 23: There were 2 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Number of degrees of freedom in T-Coupling group rest is 9.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: There were 2 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Number of degrees of freedom in T-Coupling group rest is 9.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 18.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 23: NVE simulation: will use the initial temperature of 135.187 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 23: Setting the LD random seed to -370878725 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: Setting the LD random seed to -84420627 23: 23: Generated 3 of the 3 non-bonded parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'butane' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/angles1.gro' 23: Analysing residue names: 23: There are: 1 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: Setting the LD random seed to -70289 23: 23: Generated 1 of the 1 non-bonded parameter combinations 23: 23: Excluding 1 bonded neighbours molecule type 'Argon' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon5832.gro' 23: Analysing residue names: 23: There are: 5832 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: Setting the LD random seed to -78266897 23: 23: Generated 1 of the 1 non-bonded parameter combinations 23: 23: Excluding 1 bonded neighbours molecule type 'ArgonA' 23: 23: Excluding 1 bonded neighbours molecule type 'ArgonB' 23: 23: Excluding 1 bonded neighbours molecule type 'ArgonC' 23: 23: Excluding 1 bonded neighbours molecule type 'ArgonD' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: This run will generate roughly 0 Mb of data 23: Setting the LD random seed to -102041665 23: 23: Generated 1 of the 1 non-bonded parameter combinations 23: 23: Excluding 1 bonded neighbours molecule type 'Dipole' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 23: Analysing residue names: 23: There are: 2 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: This run will generate roughly 0 Mb of data 23: Setting the LD random seed to 1538117543 23: 23: Generated 331705 of the 331705 non-bonded parameter combinations 23: 23: Generated 331705 of the 331705 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Excluding 3 bonded neighbours molecule type 'methane' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc_and_methane.gro' 23: Analysing residue names: 23: There are: 1 Water residues 23: There are: 1 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] PlumedOptionsTest.setTopology (212 ms) 23: [----------] 8 tests from PlumedOptionsTest (213 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 8 tests from 1 test suite ran. (213 ms total) 23: [ PASSED ] 8 tests. 23/96 Test #23: PlumedAppliedForcesUnitTests ................. Passed 0.53 sec test 24 Start 24: PlumedMDTests 24: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/PlumedMDTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/plumed/tests 24: Test timeout computed to be: 600 24: [==========] Running 2 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 2 tests from SimplePlumedMD/PlumedRun 24: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 24: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 24: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 24: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 24: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 24: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 24: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 2 tests from 1 test suite ran. (4 ms total) 24: [ PASSED ] 0 tests. 24: [ SKIPPED ] 2 tests, listed below: 24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 24: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 24/96 Test #24: PlumedMDTests ................................ Passed 0.12 sec test 25 Start 25: NNPotAppliedForcesUnitTest 25: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 1 test from NNPotTest 25: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 25: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 25: [----------] 1 test from NNPotTest (0 ms total) 25: 25: [----------] 5 tests from NNPotOptionsTest 25: [ RUN ] NNPotOptionsTest.DefaultParameters 25: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 25: [ RUN ] NNPotOptionsTest.OptionSetsActive 25: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 25: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 25: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 25: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 25: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 25: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 25: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 25: [----------] 5 tests from NNPotOptionsTest (0 ms total) 25: 25: [----------] 5 tests from NNPotTopologyPreprocessorTest 25: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 25: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 25: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Setting the LD random seed to -1147142145 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (3 ms) 25: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Setting the LD random seed to 795703551 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (2 ms) 25: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 63.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 25: NVE simulation: will use the initial temperature of 129.093 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Setting the LD random seed to -1100538451 25: 25: Generated 2145 of the 2145 non-bonded parameter combinations 25: 25: Generated 2145 of the 2145 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 25: Analysing residue names: 25: There are: 3 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (7 ms) 25: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: 25: NOTE 2 [file unknown]: 25: You are using constraints on all bonds, whereas the forcefield has been 25: parametrized only with constraints involving hydrogen atoms. We suggest 25: using constraints = h-bonds instead, this will also improve performance. 25: 25: 25: NOTE 3 [file unknown]: 25: For energy conservation with LINCS, lincs_iter should be 2 or larger. 25: 25: 25: Number of degrees of freedom in T-Coupling group rest is 42.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 25: NVE simulation: will use the initial temperature of 193.640 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 5 NOTEs 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 25: Setting the LD random seed to -16976705 25: 25: Generated 2145 of the 2145 non-bonded parameter combinations 25: 25: Generated 2145 of the 2145 1-4 parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 25: 25: turning all bonds into constraints... 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 25: Analysing residue names: 25: There are: 3 Protein residues 25: Analysing Protein... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (7 ms) 25: [----------] 5 tests from NNPotTopologyPreprocessorTest (20 ms total) 25: 25: [----------] 1 test from NNPotForceProviderTest 25: [ RUN ] NNPotForceProviderTest.CanConstruct 25: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 25: [----------] 1 test from NNPotForceProviderTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test suites ran. (21 ms total) 25: [ PASSED ] 12 tests. 25/96 Test #25: NNPotAppliedForcesUnitTest ................... Passed 0.10 sec test 26 Start 26: AppliedForcesUnitTest 26: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/applied_forces/tests 26: Test timeout computed to be: 30 26: [==========] Running 3 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from ElectricFieldTest 26: [ RUN ] ElectricFieldTest.Static 26: [ OK ] ElectricFieldTest.Static (0 ms) 26: [ RUN ] ElectricFieldTest.Oscillating 26: [ OK ] ElectricFieldTest.Oscillating (0 ms) 26: [ RUN ] ElectricFieldTest.Pulsed 26: [ OK ] ElectricFieldTest.Pulsed (0 ms) 26: [----------] 3 tests from ElectricFieldTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 3 tests from 1 test suite ran. (0 ms total) 26: [ PASSED ] 3 tests. 26/96 Test #26: AppliedForcesUnitTest ........................ Passed 0.07 sec test 27 Start 27: ListedForcesTest 27: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/ListedForcesTest.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/listed_forces/tests 27: Test timeout computed to be: 30 27: [==========] Running 132 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 24 tests from Bond/ListedForcesTest 27: [ RUN ] Bond/ListedForcesTest.Ifunc/0 27: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/1 27: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/2 27: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/3 27: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/4 27: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/5 27: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/6 27: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/7 27: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/8 27: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/9 27: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/10 27: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/11 27: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/12 27: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/13 27: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/14 27: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/15 27: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/16 27: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/17 27: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/18 27: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/19 27: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/20 27: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/21 27: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/22 27: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 27: [ RUN ] Bond/ListedForcesTest.Ifunc/23 27: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 27: [----------] 24 tests from Bond/ListedForcesTest (2 ms total) 27: 27: [----------] 33 tests from Angle/ListedForcesTest 27: [ RUN ] Angle/ListedForcesTest.Ifunc/0 27: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/1 27: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/2 27: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/3 27: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/4 27: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/5 27: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/6 27: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/7 27: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/8 27: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/9 27: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/10 27: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/11 27: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/12 27: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/13 27: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/14 27: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/15 27: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/16 27: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/17 27: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/18 27: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/19 27: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/20 27: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/21 27: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/22 27: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/23 27: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/24 27: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/25 27: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/26 27: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/27 27: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/28 27: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/29 27: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/30 27: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/31 27: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 27: [ RUN ] Angle/ListedForcesTest.Ifunc/32 27: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 27: [----------] 33 tests from Angle/ListedForcesTest (3 ms total) 27: 27: [----------] 18 tests from Dihedral/ListedForcesTest 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 27: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 27: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 27: [----------] 18 tests from Dihedral/ListedForcesTest (1 ms total) 27: 27: [----------] 12 tests from Polarize/ListedForcesTest 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 27: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 27: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 27: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 27: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 27: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 27: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 27: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 27: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 27: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 27: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 27: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 27: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 27: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 27: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 27: 27: [----------] 18 tests from Restraints/ListedForcesTest 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 27: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 27: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 27: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 27: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 27: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 27: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 27: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 27: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 27: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 27: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 27: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 27: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 27: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 27: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 27: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 27: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 27: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 27: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 27: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 27: [----------] 18 tests from Restraints/ListedForcesTest (1 ms total) 27: 27: [----------] 3 tests from BondZeroLength/ListedForcesTest 27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 27: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 27: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 27: 27: [----------] 3 tests from AngleZero/ListedForcesTest 27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 27: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 27: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 27: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 27: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 27: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 27: 27: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 27: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 27: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 27: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 27: 27: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 27: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 27: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 27: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 132 tests from 9 test suites ran. (12 ms total) 27: [ PASSED ] 132 tests. 27/96 Test #27: ListedForcesTest ............................. Passed 0.10 sec test 28 Start 28: NbnxmTests 28: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbnxmTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests 28: Test timeout computed to be: 30 28: [==========] Running 383 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 18 tests from KernelSetupTest 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 28: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 28: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 28: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 28: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 28: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 28: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 28: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 28: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 28: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 28: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 28: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 28: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 28: [----------] 18 tests from KernelSetupTest (0 ms total) 28: 28: [----------] 2 tests from SimdEnergyAccumulatorTest 28: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 28: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 28: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 28: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 28: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 28: 28: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 28: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 28: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 28: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 28: 28: [----------] 360 tests from Combinations/NbnxmKernelTest 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 28: Analytical Ewald is not implemented for the plain-C kernel, skip this test 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 28: There are no combination rule versions of the plain-C kernel 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (1 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 28: Cannot test or generate data for 2xNN kernels without suitable SIMD support 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 28: [----------] 360 tests from Combinations/NbnxmKernelTest (358 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 383 tests from 4 test suites ran. (359 ms total) 28: [ PASSED ] 185 tests. 28: [ SKIPPED ] 198 tests, listed below: 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 28: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 28/96 Test #28: NbnxmTests ................................... Passed 0.44 sec test 29 Start 29: NbnxmGpuTests 29: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/NbnxmGpuTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/nbnxm/tests 29: Test timeout computed to be: 30 29: [==========] Running 0 tests from 0 test suites. 29: [==========] 0 tests from 0 test suites ran. (0 ms total) 29: [ PASSED ] 0 tests. 29/96 Test #29: NbnxmGpuTests ................................ Passed 0.08 sec test 30 Start 30: CommandLineUnitTests 30: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests 30: Test timeout computed to be: 30 30: [==========] Running 60 tests from 7 test suites. 30: [----------] Global test environment set-up. 30: [----------] 3 tests from CommandLineHelpModuleTest 30: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 30: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 30: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 30: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 30: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 30: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 30: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 30: 30: [----------] 7 tests from CommandLineHelpWriterTest 30: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 30: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 30: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 30: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 30: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 30: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 30: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 30: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 30: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 30: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 30: 30: [----------] 6 tests from CommandLineModuleManagerTest 30: [ RUN ] CommandLineModuleManagerTest.RunsModule 30: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 30: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 30: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 30: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 30: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 30: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 30: 30: [----------] 13 tests from CommandLineParserTest 30: [ RUN ] CommandLineParserTest.HandlesSingleValues 30: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 30: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 30: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 30: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 30: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 30: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesString 30: [ OK ] CommandLineParserTest.HandlesString (0 ms) 30: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 30: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 30: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 30: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 30: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 30: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 30: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 30: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 30: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 30: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 30: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 30: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 30: [----------] 13 tests from CommandLineParserTest (0 ms total) 30: 30: [----------] 6 tests from CommandLineProgramContextTest 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 30: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 30: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 30: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 30: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 30: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 30: 30: [----------] 3 tests from OutputNamesTest 30: [ RUN ] OutputNamesTest.CanBeSuffixed 30: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 30: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 30: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 30: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 30: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 30: [----------] 3 tests from OutputNamesTest (0 ms total) 30: 30: [----------] 22 tests from ParseCommonArgsTest 30: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 30: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 30: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 30: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 30: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 30: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 30: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 30: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 30: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 30: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 30: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 30: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 30: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 30: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 30: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 30: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 30: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 30: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 30: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 30: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 30: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 30: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 30: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 30: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 30: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 30: Value is /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 30: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 30: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 30: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 30: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 30: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 30: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 30: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 30: [----------] 22 tests from ParseCommonArgsTest (1 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 60 tests from 7 test suites ran. (4 ms total) 30: [ PASSED ] 60 tests. 30/96 Test #30: CommandLineUnitTests ......................... Passed 0.12 sec test 31 Start 31: DomDecTests 31: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/DomDecTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests 31: Test timeout computed to be: 30 31: [==========] Running 9 tests from 2 test suites. 31: [----------] Global test environment set-up. 31: [----------] 7 tests from HashedMap 31: [ RUN ] HashedMap.InsertsFinds 31: [ OK ] HashedMap.InsertsFinds (0 ms) 31: [ RUN ] HashedMap.NegativeKeysWork 31: [ OK ] HashedMap.NegativeKeysWork (0 ms) 31: [ RUN ] HashedMap.InsertsErases 31: [ OK ] HashedMap.InsertsErases (0 ms) 31: [ RUN ] HashedMap.InsertsOrAssigns 31: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 31: [ RUN ] HashedMap.Clears 31: [ OK ] HashedMap.Clears (0 ms) 31: [ RUN ] HashedMap.LinkedEntries 31: [ OK ] HashedMap.LinkedEntries (0 ms) 31: [ RUN ] HashedMap.ResizesTable 31: [ OK ] HashedMap.ResizesTable (0 ms) 31: [----------] 7 tests from HashedMap (0 ms total) 31: 31: [----------] 2 tests from LocalAtomSetManager 31: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 31: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 31: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 31: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 31: [----------] 2 tests from LocalAtomSetManager (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 9 tests from 2 test suites ran. (0 ms total) 31: [ PASSED ] 9 tests. 31/96 Test #31: DomDecTests .................................. Passed 0.07 sec test 32 Start 32: DomDecMpiTests 32: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/domdec/tests 32: Test timeout computed to be: 30 32: [==========] Running 4 tests from 1 test suite. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from HaloExchangeTest 32: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 32: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) 32: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 32: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) 32: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 32: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 32: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 32: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) 32: [----------] 4 tests from HaloExchangeTest (0 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 4 tests from 1 test suite ran. (5 ms total) 32: [ PASSED ] 4 tests. 32/96 Test #32: DomDecMpiTests ............................... Passed 0.50 sec test 33 Start 33: EwaldUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/ewald/tests 33: Test timeout computed to be: 30 33: [==========] Running 407 tests from 9 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from SeparatePmeRanksPermittedTest 33: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 33: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 33: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 33: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 33: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 33: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 33: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 33: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 33: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 33: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 33: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 33: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 33: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 33: 33: [----------] 108 tests from Pme_SplineAndSpreadTest 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 33: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 33: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 33: [----------] 108 tests from Pme_SplineAndSpreadTest (79 ms total) 33: 33: [----------] 64 tests from Pme_SolveTest 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [----------] 64 tests from Pme_SolveTest (8 ms total) 33: 33: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (3 ms total) 33: 33: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 33: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 33: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (4 ms total) 33: 33: [----------] 64 tests from PmeDiffEps_SolveTest 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 33: Test is being skipped because: 33: CPU PME solve does not implement XYZ grid ordering 33: 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 33: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 33: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 33: [----------] 64 tests from PmeDiffEps_SolveTest (7 ms total) 33: 33: [----------] 72 tests from Pme_GatherTest 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 33: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 33: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 33: [----------] 72 tests from Pme_GatherTest (9 ms total) 33: 33: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (0 ms) 33: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 33: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 33: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 33: 33: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 33: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 33: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 33: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (23 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 407 tests from 9 test suites ran. (136 ms total) 33: [ PASSED ] 311 tests. 33: [ SKIPPED ] 96 tests, listed below: 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 33: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 33/96 Test #33: EwaldUnitTests ............................... Passed 0.43 sec test 34 Start 34: FFTUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/FFTUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fft/tests 34: Test timeout computed to be: 1920 34: [==========] Running 15 tests from 4 test suites. 34: [----------] Global test environment set-up. 34: [----------] 2 tests from ManyFFTTest 34: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 34: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (2 ms) 34: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 34: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (3 ms) 34: [----------] 2 tests from ManyFFTTest (6 ms total) 34: 34: [----------] 1 test from FFTTest 34: [ RUN ] FFTTest.Real2DLength18_15Test 34: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 34: [----------] 1 test from FFTTest (1 ms total) 34: 34: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 34: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 34: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 34: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 34: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (8 ms total) 34: 34: [----------] 2 tests from Works/ParameterizedFFTTest3D 34: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 34: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 34: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 34: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 34: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 15 tests from 4 test suites ran. (17 ms total) 34: [ PASSED ] 15 tests. 34/96 Test #34: FFTUnitTests ................................. Passed 0.22 sec test 35 Start 35: GpuUtilsUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gpu_utils/tests 35: Test timeout computed to be: 30 35: [==========] Running 67 tests from 22 test suites. 35: [----------] Global test environment set-up. 35: [----------] 2 tests from ClfftInitializer 35: [ RUN ] ClfftInitializer.SingleInitializationWorks 35: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 35: [ RUN ] ClfftInitializer.TwoInitializationsWork 35: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 35: [----------] 2 tests from ClfftInitializer (0 ms total) 35: 35: [----------] 1 test from DevicesAvailable 35: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 35: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 35: [----------] 1 test from DevicesAvailable (0 ms total) 35: 35: [----------] 1 test from DeviceStreamManagerTest 35: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 35: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 35: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 35: 35: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 35: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 35: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 35: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 35: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 35: 35: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 35: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 35: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 35: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 35: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 35: 35: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 35: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 35: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 35: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 35: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 35: 35: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 35: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 35: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 35: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 35: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 35: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 35: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 35: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 35: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 35: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 35: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 35: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 35: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 35: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 35: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 35: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 35: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 35: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 35: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 35: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 35: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 35: 35: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 35: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 35: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 35: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 35: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/0.Swap 35: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/0.Comparison 35: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 35: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 35: 35: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 35: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 35: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 35: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 35: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/1.Swap 35: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/1.Comparison 35: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 35: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 35: 35: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 35: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 35: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 35: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 35: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/2.Swap 35: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/2.Comparison 35: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 35: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 35: 35: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 35: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 35: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 35: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 35: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/3.Swap 35: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 35: [ RUN ] HostAllocatorTestNoMem/3.Comparison 35: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 35: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 35: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 35: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 35: 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 35: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 35: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 35: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 35: 35: [----------] 1 test from HostAllocatorUntypedTest 35: [ RUN ] HostAllocatorUntypedTest.Comparison 35: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 35: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 35: 35: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 35: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 35: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 35: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 35: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/0.Move 35: [ OK ] AllocatorTest/0.Move (0 ms) 35: [----------] 4 tests from AllocatorTest/0 (0 ms total) 35: 35: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 35: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 35: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 35: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 35: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/1.Move 35: [ OK ] AllocatorTest/1.Move (0 ms) 35: [----------] 4 tests from AllocatorTest/1 (0 ms total) 35: 35: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 35: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 35: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 35: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 35: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/2.Move 35: [ OK ] AllocatorTest/2.Move (0 ms) 35: [----------] 4 tests from AllocatorTest/2 (0 ms total) 35: 35: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 35: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 35: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 35: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 35: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 35: [ RUN ] AllocatorTest/3.Move 35: [ OK ] AllocatorTest/3.Move (0 ms) 35: [----------] 4 tests from AllocatorTest/3 (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 67 tests from 22 test suites ran. (0 ms total) 35: [ PASSED ] 67 tests. 35/96 Test #35: GpuUtilsUnitTests ............................ Passed 0.08 sec test 36 Start 36: HardwareUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/hardware/tests 36: Test timeout computed to be: 30 36: [==========] Running 22 tests from 10 test suites. 36: [----------] Global test environment set-up. 36: [----------] 1 test from CpuInfoTest 36: [ RUN ] CpuInfoTest.SupportLevel 36: [ OK ] CpuInfoTest.SupportLevel (0 ms) 36: [----------] 1 test from CpuInfoTest (0 ms total) 36: 36: [----------] 4 tests from HardwareTopologyTest 36: [ RUN ] HardwareTopologyTest.Execute 36: [ OK ] HardwareTopologyTest.Execute (3 ms) 36: [ RUN ] HardwareTopologyTest.HwlocExecute 36: [ OK ] HardwareTopologyTest.HwlocExecute (3 ms) 36: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 36: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (3 ms) 36: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 36: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (3 ms) 36: [----------] 4 tests from HardwareTopologyTest (15 ms total) 36: 36: [----------] 1 test from DevicesManagerTest 36: [ RUN ] DevicesManagerTest.Serialization 36: [ OK ] DevicesManagerTest.Serialization (0 ms) 36: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 36: [----------] 1 test from DevicesManagerTest (0 ms total) 36: 36: [----------] 1 test from UuidStringTest 36: [ RUN ] UuidStringTest.Works 36: [ OK ] UuidStringTest.Works (0 ms) 36: [----------] 1 test from UuidStringTest (0 ms total) 36: 36: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 36: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 36: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 36: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (2 ms total) 36: 36: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 36: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 36: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 36: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 36: 36: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 36: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 36: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 36: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 36: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 36: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 36: 36: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 36: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 36: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 36: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 36: 36: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 36: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 36: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 36: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (0 ms total) 36: 36: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 36: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 36: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 36: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 22 tests from 10 test suites ran. (25 ms total) 36: [ PASSED ] 22 tests. 36: 36: YOU HAVE 1 DISABLED TEST 36: 36/96 Test #36: HardwareUnitTests ............................ Passed 0.12 sec test 37 Start 37: MathUnitTests 37: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MathUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/math/tests 37: Test timeout computed to be: 30 37: [==========] Running 328 tests from 41 test suites. 37: [----------] Global test environment set-up. 37: [----------] 1 test from EmptyArrayRefWithPaddingTest 37: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 37: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 37: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 37: 37: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 37: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 37: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 37: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 37: 37: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 37: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 37: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 37: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 37: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 37: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 37: 37: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 37: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 37: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 37: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 37: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 37: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 37: 37: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 37: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 37: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 37: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 37: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 37: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 37: 37: [----------] 2 tests from InvertBoxMatrixTest 37: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 37: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 37: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 37: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 37: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 37: 37: [----------] 8 tests from ComplexNumberTest 37: [ RUN ] ComplexNumberTest.RealComplexMultiply 37: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 37: [ RUN ] ComplexNumberTest.RealComplexExp 37: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexAdd 37: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexSubtract 37: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexMultiply 37: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexDivision 37: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexConjugate 37: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 37: [ RUN ] ComplexNumberTest.ComplexAbs2 37: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 37: [----------] 8 tests from ComplexNumberTest (0 ms total) 37: 37: [----------] 11 tests from TranslateAndScaleTest 37: [ RUN ] TranslateAndScaleTest.identityTransformation 37: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 37: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 37: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 37: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 37: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 37: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 37: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 37: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingIdentity 37: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 37: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 37: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 37: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 37: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 37: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 37: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 37: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 37: 37: [----------] 3 tests from AffineTransformationTest 37: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 37: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 37: [ RUN ] AffineTransformationTest.applyTransformationToVectors 37: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 37: [ RUN ] AffineTransformationTest.retrieveGradient 37: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 37: [----------] 3 tests from AffineTransformationTest (0 ms total) 37: 37: [----------] 14 tests from DensitySimilarityTest 37: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 37: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 37: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 37: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 37: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 37: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 37: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 37: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 37: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 37: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 37: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 37: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 37: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (20 ms) 37: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 37: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (25 ms) 37: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 37: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 37: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 37: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.NormalizationCorrect 37: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 37: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 37: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 37: [----------] 14 tests from DensitySimilarityTest (47 ms total) 37: 37: [----------] 6 tests from StructureSimilarityTest 37: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 37: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 37: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 37: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 37: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 37: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 37: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 37: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 37: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 37: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 37: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 37: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 37: [----------] 6 tests from StructureSimilarityTest (0 ms total) 37: 37: [----------] 8 tests from ExponentialMovingAverage 37: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 37: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 37: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 37: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 37: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 37: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 37: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 37: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 37: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 37: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 37: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 37: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 37: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 37: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 37: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 37: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 37: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 37: 37: [----------] 21 tests from FunctionTest 37: [ RUN ] FunctionTest.StaticLog2 37: [ OK ] FunctionTest.StaticLog2 (0 ms) 37: [ RUN ] FunctionTest.Log2I32Bit 37: [ OK ] FunctionTest.Log2I32Bit (0 ms) 37: [ RUN ] FunctionTest.Log2I64Bit 37: [ OK ] FunctionTest.Log2I64Bit (0 ms) 37: [ RUN ] FunctionTest.GreatestCommonDivisor 37: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 37: [ RUN ] FunctionTest.InvsqrtFloat 37: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 37: [ RUN ] FunctionTest.InvsqrtDouble 37: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 37: [ RUN ] FunctionTest.InvsqrtInteger 37: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 37: [ RUN ] FunctionTest.InvcbrtFloat 37: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 37: [ RUN ] FunctionTest.InvcbrtDouble 37: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 37: [ RUN ] FunctionTest.InvcbrtInteger 37: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 37: [ RUN ] FunctionTest.SixthrootFloat 37: [ OK ] FunctionTest.SixthrootFloat (0 ms) 37: [ RUN ] FunctionTest.SixthrootDouble 37: [ OK ] FunctionTest.SixthrootDouble (0 ms) 37: [ RUN ] FunctionTest.SixthrootInteger 37: [ OK ] FunctionTest.SixthrootInteger (0 ms) 37: [ RUN ] FunctionTest.InvsixthrootFloat 37: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 37: [ RUN ] FunctionTest.InvsixthrootDouble 37: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 37: [ RUN ] FunctionTest.InvsixthrootInteger 37: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 37: [ RUN ] FunctionTest.Powers 37: [ OK ] FunctionTest.Powers (0 ms) 37: [ RUN ] FunctionTest.ErfInvFloat 37: [ OK ] FunctionTest.ErfInvFloat (0 ms) 37: [ RUN ] FunctionTest.ErfInvDouble 37: [ OK ] FunctionTest.ErfInvDouble (0 ms) 37: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 37: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 37: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 37: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 37: [----------] 21 tests from FunctionTest (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 37: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 37: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 37: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 37: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 37: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 37: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 37: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 37: 37: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 37: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 37: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 37: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 37: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 37: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 37: 37: [----------] 4 tests from GaussianOn1DLattice 37: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 37: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 37: [ RUN ] GaussianOn1DLattice.isCorrect 37: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 37: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 37: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 37: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 37: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 37: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 37: 37: [----------] 9 tests from GaussTransformTest 37: [ RUN ] GaussTransformTest.isZeroUponConstruction 37: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 37: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 37: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 37: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 37: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 37: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 37: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 37: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 37: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 37: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 37: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 37: [ RUN ] GaussTransformTest.view 37: [ OK ] GaussTransformTest.view (0 ms) 37: [----------] 9 tests from GaussTransformTest (0 ms total) 37: 37: [----------] 3 tests from DensityFittingForce 37: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 37: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 37: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 37: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 37: [ RUN ] DensityFittingForce.pullsTowardsDerivative 37: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 37: [----------] 3 tests from DensityFittingForce (0 ms total) 37: 37: [----------] 2 tests from InvertMatrixTest 37: [ RUN ] InvertMatrixTest.IdentityIsImpotent 37: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 37: [ RUN ] InvertMatrixTest.ComputesInverse 37: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 37: [----------] 2 tests from InvertMatrixTest (0 ms total) 37: 37: [----------] 22 tests from MatrixTest 37: [ RUN ] MatrixTest.canSetFromArray 37: [ OK ] MatrixTest.canSetFromArray (0 ms) 37: [ RUN ] MatrixTest.canSetStaticallyFromList 37: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 37: [ RUN ] MatrixTest.canConstructAndFill 37: [ OK ] MatrixTest.canConstructAndFill (0 ms) 37: [ RUN ] MatrixTest.canSetValues 37: [ OK ] MatrixTest.canSetValues (0 ms) 37: [ RUN ] MatrixTest.canCopyAssign 37: [ OK ] MatrixTest.canCopyAssign (0 ms) 37: [ RUN ] MatrixTest.canSwap 37: [ OK ] MatrixTest.canSwap (0 ms) 37: [ RUN ] MatrixTest.staticMultiDimArrayExtent 37: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 37: [ RUN ] MatrixTest.canAddMatrix 37: [ OK ] MatrixTest.canAddMatrix (0 ms) 37: [ RUN ] MatrixTest.canSubstractMatrix 37: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 37: [ RUN ] MatrixTest.canNegateMatrix 37: [ OK ] MatrixTest.canNegateMatrix (0 ms) 37: [ RUN ] MatrixTest.determinantWorks 37: [ OK ] MatrixTest.determinantWorks (0 ms) 37: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 37: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 37: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 37: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 37: [ RUN ] MatrixTest.traceWorks 37: [ OK ] MatrixTest.traceWorks (0 ms) 37: [ RUN ] MatrixTest.transposeWorks 37: [ OK ] MatrixTest.transposeWorks (0 ms) 37: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 37: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 37: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 37: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 37: [ RUN ] MatrixTest.canFillLegacyMatrix 37: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 37: [ RUN ] MatrixTest.IdentityMatrix 37: [ OK ] MatrixTest.IdentityMatrix (0 ms) 37: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 37: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 37: [ RUN ] MatrixTest.MatrixMatrixMultiplication 37: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 37: [ RUN ] MatrixTest.MatrixVectorMultiplication 37: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 37: [----------] 22 tests from MatrixTest (0 ms total) 37: 37: [----------] 25 tests from MultiDimArrayTest 37: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 37: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 37: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 37: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 37: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 37: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 37: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 37: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 37: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 37: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 37: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 37: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 37: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.canSwapStatic 37: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 37: [ RUN ] MultiDimArrayTest.canSwapDynamic 37: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 37: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 37: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 37: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 37: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 37: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 37: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 37: [ RUN ] MultiDimArrayTest.conversionToView 37: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 37: [ RUN ] MultiDimArrayTest.conversionToConstView 37: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 37: [ RUN ] MultiDimArrayTest.viewBegin 37: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 37: [ RUN ] MultiDimArrayTest.viewEnd 37: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 37: [ RUN ] MultiDimArrayTest.constViewConstBegin 37: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 37: [ RUN ] MultiDimArrayTest.constViewConstEnd 37: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 37: [----------] 25 tests from MultiDimArrayTest (0 ms total) 37: 37: [----------] 4 tests from MultiDimArrayToMdSpanTest 37: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 37: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 37: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 37: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 37: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 37: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 37: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 37: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 37: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 37: 37: [----------] 9 tests from NelderMeadSimplexTest 37: [ RUN ] NelderMeadSimplexTest.BestVertex 37: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 37: [ RUN ] NelderMeadSimplexTest.WorstVertex 37: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 37: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 37: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 37: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 37: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 37: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 37: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 37: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 37: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 37: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 37: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 37: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 37: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 37: [ RUN ] NelderMeadSimplexTest.OrientedLength 37: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 37: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 37: 37: [----------] 2 tests from NelderMead 37: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 37: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (10 ms) 37: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 37: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 37: [----------] 2 tests from NelderMead (11 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 37: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.ResizeWorks 37: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.ReserveWorks 37: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/0.CanCopyAssign 37: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/0.CanMoveAssign 37: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/0.CanSwap 37: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 37: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.ResizeWorks 37: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.ReserveWorks 37: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/1.CanCopyAssign 37: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/1.CanMoveAssign 37: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/1.CanSwap 37: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 37: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.ResizeWorks 37: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.ReserveWorks 37: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/2.CanCopyAssign 37: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/2.CanMoveAssign 37: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/2.CanSwap 37: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 37: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.ResizeWorks 37: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.ReserveWorks 37: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/3.CanCopyAssign 37: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/3.CanMoveAssign 37: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/3.CanSwap 37: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 37: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.ResizeWorks 37: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.ReserveWorks 37: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/4.CanCopyAssign 37: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/4.CanMoveAssign 37: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/4.CanSwap 37: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 37: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.ResizeWorks 37: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.ReserveWorks 37: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/5.CanCopyAssign 37: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/5.CanMoveAssign 37: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/5.CanSwap 37: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 37: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.ResizeWorks 37: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.ReserveWorks 37: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/6.CanCopyAssign 37: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/6.CanMoveAssign 37: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/6.CanSwap 37: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 37: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.ResizeWorks 37: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.ReserveWorks 37: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/7.CanCopyAssign 37: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/7.CanMoveAssign 37: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/7.CanSwap 37: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 37: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.ResizeWorks 37: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.ReserveWorks 37: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/8.CanCopyAssign 37: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/8.CanMoveAssign 37: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/8.CanSwap 37: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 37: 37: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 37: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 37: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.ResizeWorks 37: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.ReserveWorks 37: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 37: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 37: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 37: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 37: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 37: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 37: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 37: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 37: [ RUN ] PaddedVectorTest/9.CanCopyAssign 37: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 37: [ RUN ] PaddedVectorTest/9.CanMoveAssign 37: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 37: [ RUN ] PaddedVectorTest/9.CanSwap 37: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 37: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 37: 37: [----------] 41 tests from RVecTest 37: [ RUN ] RVecTest.CanBeStoredInVector 37: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 37: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 37: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 37: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 37: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 37: [ RUN ] RVecTest.WorksAsMutable_rvec 37: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 37: [ RUN ] RVecTest.WorksAs_rvec_Array 37: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 37: [ RUN ] RVecTest.ComparesEqual 37: [ OK ] RVecTest.ComparesEqual (0 ms) 37: [ RUN ] RVecTest.ComparesUnequal 37: [ OK ] RVecTest.ComparesUnequal (0 ms) 37: [ RUN ] RVecTest.CanAddRVecToRvec 37: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 37: [ RUN ] RVecTest.CanAddAssignRVecToRvec 37: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 37: [ RUN ] RVecTest.CanSubtractRVecFromRvec 37: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 37: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 37: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 37: [ RUN ] RVecTest.CanDotProductRVecByRvec 37: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 37: [ RUN ] RVecTest.CanCrossProductRVecByRvec 37: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 37: [ RUN ] RVecTest.CanDivideRVecInplace 37: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 37: [ RUN ] RVecTest.CanScaleRVec 37: [ OK ] RVecTest.CanScaleRVec (0 ms) 37: [ RUN ] RVecTest.CanDivideRVec 37: [ OK ] RVecTest.CanDivideRVec (0 ms) 37: [ RUN ] RVecTest.CanDoUnitvFromRVec 37: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 37: [ RUN ] RVecTest.CanSqLengthOfRVec 37: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 37: [ RUN ] RVecTest.CanLengthOfRVec 37: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 37: [ RUN ] RVecTest.CanCastToRVec 37: [ OK ] RVecTest.CanCastToRVec (0 ms) 37: [ RUN ] RVecTest.CanCastToDVec 37: [ OK ] RVecTest.CanCastToDVec (0 ms) 37: [ RUN ] RVecTest.CanLeftScalarMultiply 37: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 37: [ RUN ] RVecTest.CanRightScalarMultiply 37: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 37: [ RUN ] RVecTest.CanGetUnitvFromRVec 37: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 37: [ RUN ] RVecTest.CanGetSqLengthOfRVec 37: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 37: [ RUN ] RVecTest.CanGetLengthOfRVec 37: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 37: [ RUN ] RVecTest.CanDoCrossProductOfRVec 37: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 37: [ RUN ] RVecTest.CanDoDotProductOfRVec 37: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 37: [ RUN ] RVecTest.CanScaleByVector 37: [ OK ] RVecTest.CanScaleByVector (0 ms) 37: [ RUN ] RVecTest.CanNegate 37: [ OK ] RVecTest.CanNegate (0 ms) 37: [ RUN ] RVecTest.asIVec 37: [ OK ] RVecTest.asIVec (0 ms) 37: [ RUN ] RVecTest.elementWiseMin 37: [ OK ] RVecTest.elementWiseMin (0 ms) 37: [ RUN ] RVecTest.elementWiseMax 37: [ OK ] RVecTest.elementWiseMax (0 ms) 37: [ RUN ] RVecTest.WorksAs_dvec_Reference 37: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 37: [ RUN ] RVecTest.WorksAs_ivec_Reference 37: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 37: [ RUN ] RVecTest.WorksAs_rvec_Reference 37: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 37: [ RUN ] RVecTest.CopyConstructorWorks 37: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 37: [ RUN ] RVecTest.CopyAssignmentWorks 37: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 37: [ RUN ] RVecTest.MoveConstructorWorks 37: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 37: [ RUN ] RVecTest.MoveAssignmentWorks 37: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 37: [ RUN ] RVecTest.UsableInConstexpr 37: [ OK ] RVecTest.UsableInConstexpr (0 ms) 37: [----------] 41 tests from RVecTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 328 tests from 41 test suites ran. (62 ms total) 37: [ PASSED ] 328 tests. 37/96 Test #37: MathUnitTests ................................ Passed 0.16 sec test 38 Start 38: MdrunUtilityUnitTests 38: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests 38: Test timeout computed to be: 30 38: [==========] Running 21 tests from 2 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from MDModulesNotifierTest 38: [ RUN ] MDModulesNotifierTest.AddConsumer 38: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 38: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 38: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 38: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 38: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 38: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 38: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 38: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 38: 38: [----------] 17 tests from ThreadAffinityTest 38: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 38: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 38: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 38: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 38: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 38: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 38: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 38: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 38: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 38: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 38: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 38: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 38: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 38: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 38: NOTE: Affinity setting failed. 38: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 38: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 38: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 38: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 38: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 38: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 38: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 38: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 38: NOTE: Affinity setting for 1/2 threads failed. 38: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 38: [----------] 17 tests from ThreadAffinityTest (4 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 21 tests from 2 test suites ran. (4 ms total) 38: [ PASSED ] 21 tests. 38/96 Test #38: MdrunUtilityUnitTests ........................ Passed 0.13 sec test 39 Start 39: MdrunUtilityMpiUnitTests 39: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdrunutility/tests 39: Test timeout computed to be: 30 39: [==========] Running 13 tests from 2 test suites. 39: [----------] Global test environment set-up. 39: [----------] 6 tests from ThreadAffinityMultiRankTest 39: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 39: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (55 ms) 39: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 39: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (36 ms) 39: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 39: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (31 ms) 39: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 39: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 39: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 39: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 39: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 39: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 39: [----------] 6 tests from ThreadAffinityMultiRankTest (147 ms total) 39: 39: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) 39: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 39: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) 39: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (1 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 13 tests from 2 test suites ran. (149 ms total) 39: [ PASSED ] 13 tests. 39/96 Test #39: MdrunUtilityMpiUnitTests ..................... Passed 0.49 sec test 40 Start 40: MDSpanTests 40: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MDSpanTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdspan/tests 40: Test timeout computed to be: 30 40: [==========] Running 32 tests from 7 test suites. 40: [----------] Global test environment set-up. 40: [----------] 4 tests from BasicAccessorPolicy 40: [ RUN ] BasicAccessorPolicy.Decay 40: [ OK ] BasicAccessorPolicy.Decay (0 ms) 40: [ RUN ] BasicAccessorPolicy.Access 40: [ OK ] BasicAccessorPolicy.Access (0 ms) 40: [ RUN ] BasicAccessorPolicy.Offset 40: [ OK ] BasicAccessorPolicy.Offset (0 ms) 40: [ RUN ] BasicAccessorPolicy.CopyAccessor 40: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 40: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 40: 40: [----------] 4 tests from ExtentsTest 40: [ RUN ] ExtentsTest.Construction 40: [ OK ] ExtentsTest.Construction (0 ms) 40: [ RUN ] ExtentsTest.PurelyStatic 40: [ OK ] ExtentsTest.PurelyStatic (0 ms) 40: [ RUN ] ExtentsTest.RankNought 40: [ OK ] ExtentsTest.RankNought (0 ms) 40: [ RUN ] ExtentsTest.Assignment 40: [ OK ] ExtentsTest.Assignment (0 ms) 40: [----------] 4 tests from ExtentsTest (0 ms total) 40: 40: [----------] 8 tests from MdSpanExtension 40: [ RUN ] MdSpanExtension.SlicingAllStatic 40: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 40: [ RUN ] MdSpanExtension.SlicingDynamic 40: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 40: [ RUN ] MdSpanExtension.SlicingAllStatic3D 40: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 40: [ RUN ] MdSpanExtension.SlicingEqualsView3D 40: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 40: [ RUN ] MdSpanExtension.additionWorks 40: [ OK ] MdSpanExtension.additionWorks (0 ms) 40: [ RUN ] MdSpanExtension.subtractionWorks 40: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 40: [ RUN ] MdSpanExtension.multiplicationWorks 40: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 40: [ RUN ] MdSpanExtension.divisionWorks 40: [ OK ] MdSpanExtension.divisionWorks (0 ms) 40: [----------] 8 tests from MdSpanExtension (0 ms total) 40: 40: [----------] 3 tests from LayoutTests 40: [ RUN ] LayoutTests.LayoutRightConstruction 40: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 40: [ RUN ] LayoutTests.LayoutRightProperties 40: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 40: [ RUN ] LayoutTests.LayoutRightOperator 40: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 40: [----------] 3 tests from LayoutTests (0 ms total) 40: 40: [----------] 1 test from MdSpanTest 40: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 40: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 40: [----------] 1 test from MdSpanTest (0 ms total) 40: 40: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 40: [ RUN ] MdSpanTest/0.Rank 40: [ OK ] MdSpanTest/0.Rank (0 ms) 40: [ RUN ] MdSpanTest/0.DynamicRank 40: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 40: [ RUN ] MdSpanTest/0.Extents 40: [ OK ] MdSpanTest/0.Extents (0 ms) 40: [ RUN ] MdSpanTest/0.Strides 40: [ OK ] MdSpanTest/0.Strides (0 ms) 40: [ RUN ] MdSpanTest/0.Properties 40: [ OK ] MdSpanTest/0.Properties (0 ms) 40: [ RUN ] MdSpanTest/0.Operator 40: [ OK ] MdSpanTest/0.Operator (0 ms) 40: [----------] 6 tests from MdSpanTest/0 (0 ms total) 40: 40: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 40: [ RUN ] MdSpanTest/1.Rank 40: [ OK ] MdSpanTest/1.Rank (0 ms) 40: [ RUN ] MdSpanTest/1.DynamicRank 40: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 40: [ RUN ] MdSpanTest/1.Extents 40: [ OK ] MdSpanTest/1.Extents (0 ms) 40: [ RUN ] MdSpanTest/1.Strides 40: [ OK ] MdSpanTest/1.Strides (0 ms) 40: [ RUN ] MdSpanTest/1.Properties 40: [ OK ] MdSpanTest/1.Properties (0 ms) 40: [ RUN ] MdSpanTest/1.Operator 40: [ OK ] MdSpanTest/1.Operator (0 ms) 40: [----------] 6 tests from MdSpanTest/1 (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 32 tests from 7 test suites ran. (0 ms total) 40: [ PASSED ] 32 tests. 40/96 Test #40: MDSpanTests .................................. Passed 0.08 sec test 41 Start 41: MdtypesUnitTest 41: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/mdtypes/tests 41: Test timeout computed to be: 30 41: [==========] Running 97 tests from 7 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ForeingLambdaTermsDhdl 41: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 41: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 41: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 41: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 41: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 41: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 41: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 41: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 41: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 41: 41: [----------] 4 tests from ObservablesReducerTest 41: [ RUN ] ObservablesReducerTest.CanMoveAssign 41: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 41: [ RUN ] ObservablesReducerTest.CanMoveConstruct 41: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 41: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 41: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 41: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 41: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 41: [----------] 4 tests from ObservablesReducerTest (0 ms total) 41: 41: [----------] 2 tests from CheckpointDataTest 41: [ RUN ] CheckpointDataTest.SingleDataTest 41: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 41: [ RUN ] CheckpointDataTest.MultiDataTest 41: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 41: [----------] 2 tests from CheckpointDataTest (3 ms total) 41: 41: [----------] 7 tests from ForceBuffers 41: [ RUN ] ForceBuffers.ConstructsUnpinned 41: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 41: [ RUN ] ForceBuffers.ConstructsPinned 41: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 41: [ RUN ] ForceBuffers.ConstructsEmpty 41: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 41: [ RUN ] ForceBuffers.ResizeWorks 41: [ OK ] ForceBuffers.ResizeWorks (0 ms) 41: [ RUN ] ForceBuffers.PaddingWorks 41: [ OK ] ForceBuffers.PaddingWorks (0 ms) 41: [ RUN ] ForceBuffers.CopyWorks 41: [ OK ] ForceBuffers.CopyWorks (0 ms) 41: [ RUN ] ForceBuffers.CopyDoesNotPin 41: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 41: [----------] 7 tests from ForceBuffers (0 ms total) 41: 41: [----------] 5 tests from MultipleTimeStepping 41: [ RUN ] MultipleTimeStepping.ChecksNumLevels 41: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 41: [ RUN ] MultipleTimeStepping.SelectsForceGroups 41: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 41: [ RUN ] MultipleTimeStepping.ChecksStepFactor 41: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 41: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 41: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 41: [ RUN ] MultipleTimeStepping.ChecksIntegrator 41: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 41: [----------] 5 tests from MultipleTimeStepping (0 ms total) 41: 41: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 41: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 41: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 41: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 41: 41: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 41: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 41: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 41: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 97 tests from 7 test suites ran. (4 ms total) 41: [ PASSED ] 97 tests. 41/96 Test #41: MdtypesUnitTest .............................. Passed 0.08 sec test 42 Start 42: OnlineHelpUnitTests 42: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/onlinehelp/tests 42: Test timeout computed to be: 30 42: [==========] Running 22 tests from 4 test suites. 42: [----------] Global test environment set-up. 42: [----------] 6 tests from TextTableFormatterTest 42: [ RUN ] TextTableFormatterTest.HandlesBasicCase 42: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 42: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 42: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 42: [ RUN ] TextTableFormatterTest.HandlesIndentation 42: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 42: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 42: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 42: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 42: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 42: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 42: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 42: [----------] 6 tests from TextTableFormatterTest (0 ms total) 42: 42: [----------] 3 tests from HelpManagerTest 42: [ RUN ] HelpManagerTest.HandlesRootTopic 42: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 42: [ RUN ] HelpManagerTest.HandlesSubTopics 42: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 42: [ RUN ] HelpManagerTest.HandlesInvalidTopics 42: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 42: [----------] 3 tests from HelpManagerTest (0 ms total) 42: 42: [----------] 2 tests from HelpTopicFormattingTest 42: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 42: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 42: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 42: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 42: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 42: 42: [----------] 11 tests from HelpWriterContextTest 42: [ RUN ] HelpWriterContextTest.FormatsParagraphs 42: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 42: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 42: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 42: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsLiteralText 42: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 42: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 42: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsBulletList 42: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 42: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 42: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsGridTable 42: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 42: [ RUN ] HelpWriterContextTest.FormatsTitles 42: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 42: [----------] 11 tests from HelpWriterContextTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 22 tests from 4 test suites ran. (1 ms total) 42: [ PASSED ] 22 tests. 42/96 Test #42: OnlineHelpUnitTests .......................... Passed 0.10 sec test 43 Start 43: OptionsUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/tests 43: Test timeout computed to be: 30 43: [==========] Running 112 tests from 18 test suites. 43: [----------] Global test environment set-up. 43: [----------] 5 tests from AbstractOptionStorageTest 43: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 43: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 43: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 43: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 43: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 43: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 43: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 43: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 43: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 43: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 43: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 43: 43: [----------] 10 tests from FileNameOptionTest 43: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 43: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 43: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 43: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 43: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 43: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 43: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 43: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 43: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 43: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 43: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 43: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 43: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 43: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 43: [----------] 10 tests from FileNameOptionTest (0 ms total) 43: 43: [----------] 16 tests from FileNameOptionManagerTest 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 43: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 43: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 43: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 43: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 43: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 43: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 43: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 43: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 43: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 43: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 43: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 43: 43: [----------] 1 test from OptionsTest 43: [ RUN ] OptionsTest.FailsOnNonsafeStorage 43: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 43: [----------] 1 test from OptionsTest (0 ms total) 43: 43: [----------] 9 tests from OptionsAssignerTest 43: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 43: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 43: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 43: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 43: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesMissingValue 43: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesExtraValue 43: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesGroups 43: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesSections 43: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 43: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 43: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 43: [----------] 9 tests from OptionsAssignerTest (0 ms total) 43: 43: [----------] 4 tests from OptionsAssignerBooleanTest 43: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 43: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 43: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 43: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 43: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 43: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 43: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 43: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 43: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 43: 43: [----------] 13 tests from OptionsAssignerIntegerTest 43: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 43: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 43: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 43: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 43: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 43: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 43: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 43: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 43: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 43: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 43: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 43: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 43: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 43: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 43: 43: [----------] 5 tests from OptionsAssignerDoubleTest 43: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 43: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 43: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 43: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 43: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 43: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 43: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 43: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 43: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 43: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 43: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 43: 43: [----------] 9 tests from OptionsAssignerStringTest 43: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 43: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 43: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 43: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 43: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 43: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 43: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 43: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 43: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 43: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 43: 43: [----------] 6 tests from OptionsAssignerEnumTest 43: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 43: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 43: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 43: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 43: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 43: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 43: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 43: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 43: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 43: 43: [----------] 8 tests from RepeatingOptionSectionTest 43: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 43: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 43: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 43: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 43: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 43: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 43: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 43: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 43: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 43: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 43: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 43: 43: [----------] 1 test from TimeUnitManagerTest 43: [ RUN ] TimeUnitManagerTest.BasicOperations 43: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 43: [----------] 1 test from TimeUnitManagerTest (0 ms total) 43: 43: [----------] 4 tests from TimeUnitBehaviorTest 43: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 43: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 43: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 43: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 43: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 43: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 43: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 43: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 43: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 43: 43: [----------] 2 tests from TreeValueSupportAssignTest 43: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 43: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 43: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 43: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 43: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 43: 43: [----------] 1 test from TreeValueSupportAssignErrorTest 43: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 43: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 43: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 43: 43: [----------] 5 tests from TreeValueSupportCheckTest 43: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 43: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 43: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 43: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 43: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 43: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 43: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 43: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 43: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 43: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 43: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 43: 43: [----------] 6 tests from TreeValueSupportAdjustTest 43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 43: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 43: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 43: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 43: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 43: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 43: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 43: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 43: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 43: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 43: 43: [----------] 7 tests from TreeValueSupportTest 43: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 43: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 43: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsInt64Option 43: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsStringOption 43: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsFloatOption 43: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 43: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 43: [ RUN ] TreeValueSupportTest.SupportsEnumOption 43: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 43: [----------] 7 tests from TreeValueSupportTest (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 112 tests from 18 test suites ran. (2 ms total) 43: [ PASSED ] 112 tests. 43/96 Test #43: OptionsUnitTests ............................. Passed 0.13 sec test 44 Start 44: PbcutilUnitTest 44: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pbcutil/tests 44: Test timeout computed to be: 30 44: [==========] Running 37 tests from 5 test suites. 44: [----------] Global test environment set-up. 44: [----------] 1 test from ShiftTest 44: [ RUN ] ShiftTest.CoordinateShiftWorks 44: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 44: [----------] 1 test from ShiftTest (0 ms total) 44: 44: [----------] 2 tests from MShift 44: [ RUN ] MShift.shiftsAndUnshifts 44: [ OK ] MShift.shiftsAndUnshifts (0 ms) 44: [ RUN ] MShift.shiftsAndUnshiftsSelf 44: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 44: [----------] 2 tests from MShift (0 ms total) 44: 44: [----------] 5 tests from PbcTest 44: [ RUN ] PbcTest.CalcShiftsWorks 44: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 44: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 44: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 44: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 44: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 44: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 44: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 44: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 44: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 44: [----------] 5 tests from PbcTest (0 ms total) 44: 44: [----------] 2 tests from PbcEnumsTest 44: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 44: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 44: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 44: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 44: [----------] 2 tests from PbcEnumsTest (0 ms total) 44: 44: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 44: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 44: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 44: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (2 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 37 tests from 5 test suites ran. (3 ms total) 44: [ PASSED ] 37 tests. 44/96 Test #44: PbcutilUnitTest .............................. Passed 0.31 sec test 45 Start 45: RandomUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/RandomUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/random/tests 45: Test timeout computed to be: 30 45: [==========] Running 44 tests from 10 test suites. 45: [----------] Global test environment set-up. 45: [----------] 4 tests from ExponentialDistributionTest 45: [ RUN ] ExponentialDistributionTest.Output 45: [ OK ] ExponentialDistributionTest.Output (0 ms) 45: [ RUN ] ExponentialDistributionTest.Logical 45: [ OK ] ExponentialDistributionTest.Logical (0 ms) 45: [ RUN ] ExponentialDistributionTest.Reset 45: [ OK ] ExponentialDistributionTest.Reset (0 ms) 45: [ RUN ] ExponentialDistributionTest.AltParam 45: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 45: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 45: 45: [----------] 4 tests from GammaDistributionTest 45: [ RUN ] GammaDistributionTest.Output 45: [ OK ] GammaDistributionTest.Output (0 ms) 45: [ RUN ] GammaDistributionTest.Logical 45: [ OK ] GammaDistributionTest.Logical (0 ms) 45: [ RUN ] GammaDistributionTest.Reset 45: [ OK ] GammaDistributionTest.Reset (0 ms) 45: [ RUN ] GammaDistributionTest.AltParam 45: [ OK ] GammaDistributionTest.AltParam (0 ms) 45: [----------] 4 tests from GammaDistributionTest (0 ms total) 45: 45: [----------] 4 tests from NormalDistributionTest 45: [ RUN ] NormalDistributionTest.Output 45: [ OK ] NormalDistributionTest.Output (0 ms) 45: [ RUN ] NormalDistributionTest.Logical 45: [ OK ] NormalDistributionTest.Logical (0 ms) 45: [ RUN ] NormalDistributionTest.Reset 45: [ OK ] NormalDistributionTest.Reset (0 ms) 45: [ RUN ] NormalDistributionTest.AltParam 45: [ OK ] NormalDistributionTest.AltParam (0 ms) 45: [----------] 4 tests from NormalDistributionTest (0 ms total) 45: 45: [----------] 1 test from SeedTest 45: [ RUN ] SeedTest.makeRandomSeed 45: [ OK ] SeedTest.makeRandomSeed (0 ms) 45: [----------] 1 test from SeedTest (0 ms total) 45: 45: [----------] 6 tests from TabulatedNormalDistributionTest 45: [ RUN ] TabulatedNormalDistributionTest.Output14 45: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 45: [ RUN ] TabulatedNormalDistributionTest.Output16 45: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 45: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 45: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 45: [ RUN ] TabulatedNormalDistributionTest.Logical 45: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 45: [ RUN ] TabulatedNormalDistributionTest.Reset 45: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 45: [ RUN ] TabulatedNormalDistributionTest.AltParam 45: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 45: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 45: 45: [----------] 1 test from TabulatedNormalDistributionTableTest 45: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 45: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 45: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 45: 45: [----------] 6 tests from ThreeFry2x64Test 45: [ RUN ] ThreeFry2x64Test.Logical 45: [ OK ] ThreeFry2x64Test.Logical (0 ms) 45: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 45: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 45: [ RUN ] ThreeFry2x64Test.Reseed 45: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 45: [ RUN ] ThreeFry2x64Test.Discard 45: [ OK ] ThreeFry2x64Test.Discard (0 ms) 45: [ RUN ] ThreeFry2x64Test.InvalidCounter 45: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 45: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 45: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 45: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 45: 45: [----------] 4 tests from UniformIntDistributionTest 45: [ RUN ] UniformIntDistributionTest.Output 45: [ OK ] UniformIntDistributionTest.Output (0 ms) 45: [ RUN ] UniformIntDistributionTest.Logical 45: [ OK ] UniformIntDistributionTest.Logical (0 ms) 45: [ RUN ] UniformIntDistributionTest.Reset 45: [ OK ] UniformIntDistributionTest.Reset (0 ms) 45: [ RUN ] UniformIntDistributionTest.AltParam 45: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 45: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 45: 45: [----------] 5 tests from UniformRealDistributionTest 45: [ RUN ] UniformRealDistributionTest.GenerateCanonical 45: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 45: [ RUN ] UniformRealDistributionTest.Output 45: [ OK ] UniformRealDistributionTest.Output (0 ms) 45: [ RUN ] UniformRealDistributionTest.Logical 45: [ OK ] UniformRealDistributionTest.Logical (0 ms) 45: [ RUN ] UniformRealDistributionTest.Reset 45: [ OK ] UniformRealDistributionTest.Reset (0 ms) 45: [ RUN ] UniformRealDistributionTest.AltParam 45: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 45: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 45: 45: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 45: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 45: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 45: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 44 tests from 10 test suites ran. (1 ms total) 45: [ PASSED ] 44 tests. 45/96 Test #45: RandomUnitTests .............................. Passed 0.32 sec test 46 Start 46: RestraintTests 46: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/RestraintTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/restraint/tests 46: Test timeout computed to be: 30 46: [==========] Running 1 test from 1 test suite. 46: [----------] Global test environment set-up. 46: [----------] 1 test from RestraintManager 46: [ RUN ] RestraintManager.restraintList 46: [ OK ] RestraintManager.restraintList (0 ms) 46: [----------] 1 test from RestraintManager (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 1 test from 1 test suite ran. (0 ms total) 46: [ PASSED ] 1 test. 46/96 Test #46: RestraintTests ............................... Passed 0.08 sec test 47 Start 47: TableUnitTests 47: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TableUnitTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tables/tests 47: Test timeout computed to be: 30 47: [==========] Running 20 tests from 2 test suites. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 47: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 47: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 47: [ RUN ] SplineTableTest/0.Sinc 47: [ OK ] SplineTableTest/0.Sinc (0 ms) 47: [ RUN ] SplineTableTest/0.LJ12 47: [ OK ] SplineTableTest/0.LJ12 (5 ms) 47: [ RUN ] SplineTableTest/0.PmeCorrection 47: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 47: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 47: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 47: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 47: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 47: [ RUN ] SplineTableTest/0.TwoFunctions 47: [ OK ] SplineTableTest/0.TwoFunctions (9 ms) 47: [ RUN ] SplineTableTest/0.ThreeFunctions 47: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 47: [ RUN ] SplineTableTest/0.Simd 47: [ OK ] SplineTableTest/0.Simd (2 ms) 47: [ RUN ] SplineTableTest/0.SimdTwoFunctions 47: [ OK ] SplineTableTest/0.SimdTwoFunctions (8 ms) 47: [----------] 10 tests from SplineTableTest/0 (38 ms total) 47: 47: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 47: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 47: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 47: [ RUN ] SplineTableTest/1.Sinc 47: [ OK ] SplineTableTest/1.Sinc (0 ms) 47: [ RUN ] SplineTableTest/1.LJ12 47: [ OK ] SplineTableTest/1.LJ12 (0 ms) 47: [ RUN ] SplineTableTest/1.PmeCorrection 47: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 47: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 47: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 47: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 47: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 47: [ RUN ] SplineTableTest/1.TwoFunctions 47: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 47: [ RUN ] SplineTableTest/1.ThreeFunctions 47: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 47: [ RUN ] SplineTableTest/1.Simd 47: [ OK ] SplineTableTest/1.Simd (0 ms) 47: [ RUN ] SplineTableTest/1.SimdTwoFunctions 47: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 47: [----------] 10 tests from SplineTableTest/1 (6 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 20 tests from 2 test suites ran. (44 ms total) 47: [ PASSED ] 20 tests. 47/96 Test #47: TableUnitTests ............................... Passed 0.12 sec test 48 Start 48: TaskAssignmentUnitTests 48: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/tests 48: Test timeout computed to be: 30 48: [==========] Running 3 tests from 2 test suites. 48: [----------] Global test environment set-up. 48: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 48: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 48: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 48: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 48: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 48: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 48: 48: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 48: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 48: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 48: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 3 tests from 2 test suites ran. (0 ms total) 48: [ PASSED ] 3 tests. 48/96 Test #48: TaskAssignmentUnitTests ...................... Passed 0.07 sec test 49 Start 49: GmxTimingTests 49: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxTimingTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/timing/tests 49: Test timeout computed to be: 30 49: [==========] Running 6 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 6 tests from TimingTest 49: [ RUN ] TimingTest.ElementCountingWorks 49: [ OK ] TimingTest.ElementCountingWorks (0 ms) 49: [ RUN ] TimingTest.ElementNoCountingWorks 49: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 49: [ RUN ] TimingTest.SubElementCountingWorks 49: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 49: [ RUN ] TimingTest.SubElementNoCountingWorks 49: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 49: [ RUN ] TimingTest.RunWallCycle 49: [ OK ] TimingTest.RunWallCycle (3 ms) 49: [ RUN ] TimingTest.RunWallCycleSub 49: [ OK ] TimingTest.RunWallCycleSub (0 ms) 49: [----------] 6 tests from TimingTest (3 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 6 tests from 1 test suite ran. (3 ms total) 49: [ PASSED ] 6 tests. 49/96 Test #49: GmxTimingTests ............................... Passed 0.31 sec test 50 Start 50: TopologyTest 50: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TopologyTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/topology/tests 50: Test timeout computed to be: 30 50: [==========] Running 153 tests from 10 test suites. 50: [----------] Global test environment set-up. 50: [----------] 3 tests from PdbAtomEntryTest 50: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 50: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 50: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 50: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 50: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 50: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 50: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 50: 50: [----------] 3 tests from ExclusionBlockTest 50: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 50: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 50: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 50: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 50: [ RUN ] ExclusionBlockTest.MergeExclusions 50: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 50: [----------] 3 tests from ExclusionBlockTest (0 ms total) 50: 50: [----------] 6 tests from InteractionListTest 50: [ RUN ] InteractionListTest.EmptyWorks 50: [ OK ] InteractionListTest.EmptyWorks (0 ms) 50: [ RUN ] InteractionListTest.CanAddInteractionArray 50: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 50: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 50: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 50: [ RUN ] InteractionListTest.CanAddInteractionPointer 50: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 50: [ RUN ] InteractionListTest.CanAddListToOtherList 50: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 50: [ RUN ] InteractionListTest.ClearingWorks 50: [ OK ] InteractionListTest.ClearingWorks (0 ms) 50: [----------] 6 tests from InteractionListTest (0 ms total) 50: 50: [----------] 3 tests from IndexTest 50: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 50: [ RUN ] IndexTest.WriteIndexWorks 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: [ OK ] IndexTest.WriteIndexWorks (1 ms) 50: [ RUN ] IndexTest.WriteAndReadIndexWorks 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 50: [----------] 3 tests from IndexTest (5 ms total) 50: 50: [----------] 4 tests from MtopTest 50: [ RUN ] MtopTest.RangeBasedLoop 50: [ OK ] MtopTest.RangeBasedLoop (0 ms) 50: [ RUN ] MtopTest.Operators 50: [ OK ] MtopTest.Operators (0 ms) 50: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 50: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 50: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 50: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 50: [----------] 4 tests from MtopTest (0 ms total) 50: 50: [----------] 2 tests from IListRangeTest 50: [ RUN ] IListRangeTest.RangeBasedLoopWorks 50: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 50: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 50: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 50: [----------] 2 tests from IListRangeTest (0 ms total) 50: 50: [----------] 13 tests from StringTableTest 50: [ RUN ] StringTableTest.AddSingleEntry 50: [ OK ] StringTableTest.AddSingleEntry (0 ms) 50: [ RUN ] StringTableTest.CanAccessWithAt 50: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 50: [ RUN ] StringTableTest.CanAccessWithBracket 50: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 50: [ RUN ] StringTableTest.ThrowsOutOfRange 50: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 50: [ RUN ] StringTableTest.StringCompareIsCorrect 50: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 50: [ RUN ] StringTableTest.AddTwoDistinctEntries 50: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 50: [ RUN ] StringTableTest.TryToAddDuplicates 50: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 50: [ RUN ] StringTableTest.AddLargeNumberOfEntries 50: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 50: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 50: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 50: [ RUN ] StringTableTest.CanWriteToBuffer 50: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 50: [ RUN ] StringTableTest.Roundtrip 50: [ OK ] StringTableTest.Roundtrip (0 ms) 50: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 50: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 50: [ RUN ] StringTableTest.CanCopyToLegacyTable 50: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 50: [----------] 13 tests from StringTableTest (1 ms total) 50: 50: [----------] 6 tests from LegacySymtabTest 50: [ RUN ] LegacySymtabTest.EmptyOnOpen 50: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 50: [ RUN ] LegacySymtabTest.AddSingleEntry 50: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 50: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 50: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 50: [ RUN ] LegacySymtabTest.TryToAddDuplicates 50: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 50: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 50: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 50: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 50: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 50: [----------] 6 tests from LegacySymtabTest (0 ms total) 50: 50: [----------] 5 tests from TopSortTest 50: [ RUN ] TopSortTest.WorksOnEmptyIdef 50: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 50: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 50: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 50: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 50: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 50: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 50: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 50: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 50: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 50: [----------] 5 tests from TopSortTest (0 ms total) 50: 50: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 50: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 50: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 50: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (5 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 153 tests from 10 test suites ran. (12 ms total) 50: [ PASSED ] 153 tests. 50: 50: YOU HAVE 1 DISABLED TEST 50: 50/96 Test #50: TopologyTest ................................. Passed 0.26 sec test 51 Start 51: PullTest 51: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/PullTest.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/tests 51: Test timeout computed to be: 30 51: [==========] Running 10 tests from 1 test suite. 51: [----------] Global test environment set-up. 51: [----------] 10 tests from PullTest 51: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 51: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 51: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 51: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 51: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 51: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 51: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 51: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 51: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 51: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 51: [ RUN ] PullTest.TransformationCoordSimple 51: [ OK ] PullTest.TransformationCoordSimple (0 ms) 51: [ RUN ] PullTest.TransformationCoordAdvanced 51: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 51: [ RUN ] PullTest.TransformationCoordTime 51: [ OK ] PullTest.TransformationCoordTime (0 ms) 51: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 51: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 51: [ RUN ] PullTest.TransformationCoordDummyExpression 51: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 51: [----------] 10 tests from PullTest (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 10 tests from 1 test suite ran. (0 ms total) 51: [ PASSED ] 10 tests. 51/96 Test #51: PullTest ..................................... Passed 0.19 sec test 52 Start 52: SimdUnitTests 52: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/SimdUnitTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/simd/tests 52: Test timeout computed to be: 30 52: [==========] Running 288 tests from 22 test suites. 52: [----------] Global test environment set-up. 52: [----------] 9 tests from SimdBootstrapTest 52: [ RUN ] SimdBootstrapTest.loadStore 52: [ OK ] SimdBootstrapTest.loadStore (0 ms) 52: [ RUN ] SimdBootstrapTest.loadU 52: [ OK ] SimdBootstrapTest.loadU (0 ms) 52: [ RUN ] SimdBootstrapTest.storeU 52: [ OK ] SimdBootstrapTest.storeU (0 ms) 52: [ RUN ] SimdBootstrapTest.loadStoreI 52: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 52: [ RUN ] SimdBootstrapTest.loadUI 52: [ OK ] SimdBootstrapTest.loadUI (0 ms) 52: [ RUN ] SimdBootstrapTest.storeUI 52: [ OK ] SimdBootstrapTest.storeUI (0 ms) 52: [ RUN ] SimdBootstrapTest.simd4LoadStore 52: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 52: [ RUN ] SimdBootstrapTest.simd4LoadU 52: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 52: [ RUN ] SimdBootstrapTest.simd4StoreU 52: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 52: [----------] 9 tests from SimdBootstrapTest (0 ms total) 52: 52: [----------] 41 tests from SimdScalarTest 52: [ RUN ] SimdScalarTest.load 52: [ OK ] SimdScalarTest.load (0 ms) 52: [ RUN ] SimdScalarTest.loadU 52: [ OK ] SimdScalarTest.loadU (0 ms) 52: [ RUN ] SimdScalarTest.store 52: [ OK ] SimdScalarTest.store (0 ms) 52: [ RUN ] SimdScalarTest.storeU 52: [ OK ] SimdScalarTest.storeU (0 ms) 52: [ RUN ] SimdScalarTest.setZero 52: [ OK ] SimdScalarTest.setZero (0 ms) 52: [ RUN ] SimdScalarTest.andNot 52: [ OK ] SimdScalarTest.andNot (0 ms) 52: [ RUN ] SimdScalarTest.fma 52: [ OK ] SimdScalarTest.fma (0 ms) 52: [ RUN ] SimdScalarTest.fms 52: [ OK ] SimdScalarTest.fms (0 ms) 52: [ RUN ] SimdScalarTest.fnma 52: [ OK ] SimdScalarTest.fnma (0 ms) 52: [ RUN ] SimdScalarTest.fnms 52: [ OK ] SimdScalarTest.fnms (0 ms) 52: [ RUN ] SimdScalarTest.maskAdd 52: [ OK ] SimdScalarTest.maskAdd (0 ms) 52: [ RUN ] SimdScalarTest.maskzMul 52: [ OK ] SimdScalarTest.maskzMul (0 ms) 52: [ RUN ] SimdScalarTest.maskzFma 52: [ OK ] SimdScalarTest.maskzFma (0 ms) 52: [ RUN ] SimdScalarTest.abs 52: [ OK ] SimdScalarTest.abs (0 ms) 52: [ RUN ] SimdScalarTest.max 52: [ OK ] SimdScalarTest.max (0 ms) 52: [ RUN ] SimdScalarTest.min 52: [ OK ] SimdScalarTest.min (0 ms) 52: [ RUN ] SimdScalarTest.round 52: [ OK ] SimdScalarTest.round (0 ms) 52: [ RUN ] SimdScalarTest.trunc 52: [ OK ] SimdScalarTest.trunc (0 ms) 52: [ RUN ] SimdScalarTest.reduce 52: [ OK ] SimdScalarTest.reduce (0 ms) 52: [ RUN ] SimdScalarTest.testBits 52: [ OK ] SimdScalarTest.testBits (0 ms) 52: [ RUN ] SimdScalarTest.anyTrue 52: [ OK ] SimdScalarTest.anyTrue (0 ms) 52: [ RUN ] SimdScalarTest.selectByMask 52: [ OK ] SimdScalarTest.selectByMask (0 ms) 52: [ RUN ] SimdScalarTest.selectByNotMask 52: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 52: [ RUN ] SimdScalarTest.blend 52: [ OK ] SimdScalarTest.blend (0 ms) 52: [ RUN ] SimdScalarTest.cvtR2I 52: [ OK ] SimdScalarTest.cvtR2I (0 ms) 52: [ RUN ] SimdScalarTest.cvttR2I 52: [ OK ] SimdScalarTest.cvttR2I (0 ms) 52: [ RUN ] SimdScalarTest.cvtI2R 52: [ OK ] SimdScalarTest.cvtI2R (0 ms) 52: [ RUN ] SimdScalarTest.cvtF2D 52: [ OK ] SimdScalarTest.cvtF2D (0 ms) 52: [ RUN ] SimdScalarTest.cvtD2D 52: [ OK ] SimdScalarTest.cvtD2D (0 ms) 52: [ RUN ] SimdScalarTest.loadI 52: [ OK ] SimdScalarTest.loadI (0 ms) 52: [ RUN ] SimdScalarTest.loadUI 52: [ OK ] SimdScalarTest.loadUI (0 ms) 52: [ RUN ] SimdScalarTest.storeI 52: [ OK ] SimdScalarTest.storeI (0 ms) 52: [ RUN ] SimdScalarTest.storeUI 52: [ OK ] SimdScalarTest.storeUI (0 ms) 52: [ RUN ] SimdScalarTest.andNotI 52: [ OK ] SimdScalarTest.andNotI (0 ms) 52: [ RUN ] SimdScalarTest.testBitsI 52: [ OK ] SimdScalarTest.testBitsI (0 ms) 52: [ RUN ] SimdScalarTest.selectByMaskI 52: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 52: [ RUN ] SimdScalarTest.selectByNotMaskI 52: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 52: [ RUN ] SimdScalarTest.blendI 52: [ OK ] SimdScalarTest.blendI (0 ms) 52: [ RUN ] SimdScalarTest.cvtB2IB 52: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 52: [ RUN ] SimdScalarTest.cvtIB2B 52: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 52: [ RUN ] SimdScalarTest.expandScalarsToTriplets 52: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 52: [----------] 41 tests from SimdScalarTest (0 ms total) 52: 52: [----------] 8 tests from SimdScalarUtilTest 52: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 52: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 52: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 52: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 52: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 52: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 52: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 52: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 52: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 52: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 52: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 52: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 52: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 52: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 52: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 52: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 52: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 52: 52: [----------] 37 tests from SimdScalarMathTest 52: [ RUN ] SimdScalarMathTest.copysign 52: [ OK ] SimdScalarMathTest.copysign (0 ms) 52: [ RUN ] SimdScalarMathTest.invsqrtPair 52: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 52: [ RUN ] SimdScalarMathTest.inv 52: [ OK ] SimdScalarMathTest.inv (0 ms) 52: [ RUN ] SimdScalarMathTest.maskzInvsqrt 52: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 52: [ RUN ] SimdScalarMathTest.log 52: [ OK ] SimdScalarMathTest.log (0 ms) 52: [ RUN ] SimdScalarMathTest.exp2 52: [ OK ] SimdScalarMathTest.exp2 (0 ms) 52: [ RUN ] SimdScalarMathTest.exp 52: [ OK ] SimdScalarMathTest.exp (0 ms) 52: [ RUN ] SimdScalarMathTest.erf 52: [ OK ] SimdScalarMathTest.erf (0 ms) 52: [ RUN ] SimdScalarMathTest.erfc 52: [ OK ] SimdScalarMathTest.erfc (0 ms) 52: [ RUN ] SimdScalarMathTest.sincos 52: [ OK ] SimdScalarMathTest.sincos (0 ms) 52: [ RUN ] SimdScalarMathTest.sin 52: [ OK ] SimdScalarMathTest.sin (0 ms) 52: [ RUN ] SimdScalarMathTest.cos 52: [ OK ] SimdScalarMathTest.cos (0 ms) 52: [ RUN ] SimdScalarMathTest.tan 52: [ OK ] SimdScalarMathTest.tan (0 ms) 52: [ RUN ] SimdScalarMathTest.asin 52: [ OK ] SimdScalarMathTest.asin (0 ms) 52: [ RUN ] SimdScalarMathTest.acos 52: [ OK ] SimdScalarMathTest.acos (0 ms) 52: [ RUN ] SimdScalarMathTest.atan 52: [ OK ] SimdScalarMathTest.atan (0 ms) 52: [ RUN ] SimdScalarMathTest.atan2 52: [ OK ] SimdScalarMathTest.atan2 (0 ms) 52: [ RUN ] SimdScalarMathTest.pmeForceCorrection 52: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 52: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 52: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 52: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 52: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.invSingleAccuracy 52: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 52: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.logSingleAccuracy 52: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 52: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.expSingleAccuracy 52: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 52: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 52: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 52: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 52: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 52: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 52: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 52: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 52: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 52: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 52: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 52: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 52: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 52: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 52: [----------] 37 tests from SimdScalarMathTest (0 ms total) 52: 52: [----------] 1 test from SimdTest 52: [ RUN ] SimdTest.GmxAligned 52: [ OK ] SimdTest.GmxAligned (0 ms) 52: [----------] 1 test from SimdTest (0 ms total) 52: 52: [----------] 42 tests from SimdFloatingpointTest 52: [ RUN ] SimdFloatingpointTest.setZero 52: [ OK ] SimdFloatingpointTest.setZero (0 ms) 52: [ RUN ] SimdFloatingpointTest.set 52: [ OK ] SimdFloatingpointTest.set (0 ms) 52: [ RUN ] SimdFloatingpointTest.add 52: [ OK ] SimdFloatingpointTest.add (0 ms) 52: [ RUN ] SimdFloatingpointTest.maskAdd 52: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 52: [ RUN ] SimdFloatingpointTest.sub 52: [ OK ] SimdFloatingpointTest.sub (0 ms) 52: [ RUN ] SimdFloatingpointTest.mul 52: [ OK ] SimdFloatingpointTest.mul (0 ms) 52: [ RUN ] SimdFloatingpointTest.maskzMul 52: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 52: [ RUN ] SimdFloatingpointTest.fma 52: [ OK ] SimdFloatingpointTest.fma (0 ms) 52: [ RUN ] SimdFloatingpointTest.maskzFma 52: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 52: [ RUN ] SimdFloatingpointTest.fms 52: [ OK ] SimdFloatingpointTest.fms (0 ms) 52: [ RUN ] SimdFloatingpointTest.fnma 52: [ OK ] SimdFloatingpointTest.fnma (0 ms) 52: [ RUN ] SimdFloatingpointTest.fnms 52: [ OK ] SimdFloatingpointTest.fnms (0 ms) 52: [ RUN ] SimdFloatingpointTest.abs 52: [ OK ] SimdFloatingpointTest.abs (0 ms) 52: [ RUN ] SimdFloatingpointTest.neg 52: [ OK ] SimdFloatingpointTest.neg (0 ms) 52: [ RUN ] SimdFloatingpointTest.and 52: [ OK ] SimdFloatingpointTest.and (0 ms) 52: [ RUN ] SimdFloatingpointTest.or 52: [ OK ] SimdFloatingpointTest.or (0 ms) 52: [ RUN ] SimdFloatingpointTest.xor 52: [ OK ] SimdFloatingpointTest.xor (0 ms) 52: [ RUN ] SimdFloatingpointTest.andNot 52: [ OK ] SimdFloatingpointTest.andNot (0 ms) 52: [ RUN ] SimdFloatingpointTest.max 52: [ OK ] SimdFloatingpointTest.max (0 ms) 52: [ RUN ] SimdFloatingpointTest.min 52: [ OK ] SimdFloatingpointTest.min (0 ms) 52: [ RUN ] SimdFloatingpointTest.round 52: [ OK ] SimdFloatingpointTest.round (0 ms) 52: [ RUN ] SimdFloatingpointTest.roundMode 52: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 52: [ RUN ] SimdFloatingpointTest.trunc 52: [ OK ] SimdFloatingpointTest.trunc (0 ms) 52: [ RUN ] SimdFloatingpointTest.frexp 52: [ OK ] SimdFloatingpointTest.frexp (0 ms) 52: [ RUN ] SimdFloatingpointTest.ldexp 52: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 52: [ RUN ] SimdFloatingpointTest.rsqrt 52: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 52: [ RUN ] SimdFloatingpointTest.maskzRsqrt 52: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 52: [ RUN ] SimdFloatingpointTest.rcp 52: [ OK ] SimdFloatingpointTest.rcp (0 ms) 52: [ RUN ] SimdFloatingpointTest.maskzRcp 52: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 52: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 52: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 52: [ RUN ] SimdFloatingpointTest.selectByNotMask 52: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 52: [ RUN ] SimdFloatingpointTest.cmpNe 52: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 52: [ RUN ] SimdFloatingpointTest.cmpLe 52: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 52: [ RUN ] SimdFloatingpointTest.cmpLt 52: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 52: [ RUN ] SimdFloatingpointTest.testBits 52: [ OK ] SimdFloatingpointTest.testBits (0 ms) 52: [ RUN ] SimdFloatingpointTest.andB 52: [ OK ] SimdFloatingpointTest.andB (0 ms) 52: [ RUN ] SimdFloatingpointTest.orB 52: [ OK ] SimdFloatingpointTest.orB (0 ms) 52: [ RUN ] SimdFloatingpointTest.anyTrueB 52: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 52: [ RUN ] SimdFloatingpointTest.blend 52: [ OK ] SimdFloatingpointTest.blend (0 ms) 52: [ RUN ] SimdFloatingpointTest.reduce 52: [ OK ] SimdFloatingpointTest.reduce (0 ms) 52: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 52: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 52: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 52: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 52: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 52: 52: [----------] 16 tests from SimdFloatingpointUtilTest 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 52: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 52: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 52: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 52: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 52: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 52: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 52: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 52: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 52: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 52: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 52: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 52: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 52: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 52: 52: [----------] 23 tests from SimdIntegerTest 52: [ RUN ] SimdIntegerTest.setZero 52: [ OK ] SimdIntegerTest.setZero (0 ms) 52: [ RUN ] SimdIntegerTest.set 52: [ OK ] SimdIntegerTest.set (0 ms) 52: [ RUN ] SimdIntegerTest.add 52: [ OK ] SimdIntegerTest.add (0 ms) 52: [ RUN ] SimdIntegerTest.sub 52: [ OK ] SimdIntegerTest.sub (0 ms) 52: [ RUN ] SimdIntegerTest.mul 52: [ OK ] SimdIntegerTest.mul (0 ms) 52: [ RUN ] SimdIntegerTest.and 52: [ OK ] SimdIntegerTest.and (0 ms) 52: [ RUN ] SimdIntegerTest.andNot 52: [ OK ] SimdIntegerTest.andNot (0 ms) 52: [ RUN ] SimdIntegerTest.or 52: [ OK ] SimdIntegerTest.or (0 ms) 52: [ RUN ] SimdIntegerTest.xor 52: [ OK ] SimdIntegerTest.xor (0 ms) 52: [ RUN ] SimdIntegerTest.extract 52: [ OK ] SimdIntegerTest.extract (0 ms) 52: [ RUN ] SimdIntegerTest.cvtR2I 52: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 52: [ RUN ] SimdIntegerTest.cvttR2I 52: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 52: [ RUN ] SimdIntegerTest.cvtI2R 52: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 52: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 52: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 52: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 52: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 52: [ RUN ] SimdIntegerTest.cmpLt 52: [ OK ] SimdIntegerTest.cmpLt (0 ms) 52: [ RUN ] SimdIntegerTest.testBits 52: [ OK ] SimdIntegerTest.testBits (0 ms) 52: [ RUN ] SimdIntegerTest.andB 52: [ OK ] SimdIntegerTest.andB (0 ms) 52: [ RUN ] SimdIntegerTest.orB 52: [ OK ] SimdIntegerTest.orB (0 ms) 52: [ RUN ] SimdIntegerTest.anyTrue 52: [ OK ] SimdIntegerTest.anyTrue (0 ms) 52: [ RUN ] SimdIntegerTest.blend 52: [ OK ] SimdIntegerTest.blend (0 ms) 52: [ RUN ] SimdIntegerTest.cvtB2IB 52: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 52: [ RUN ] SimdIntegerTest.cvtIB2B 52: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 52: [----------] 23 tests from SimdIntegerTest (0 ms total) 52: 52: [----------] 56 tests from SimdMathTest 52: [ RUN ] SimdMathTest.generateTestPointsFloat 52: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 52: [ RUN ] SimdMathTest.copysign 52: [ OK ] SimdMathTest.copysign (0 ms) 52: [ RUN ] SimdMathTest.invsqrt 52: [ OK ] SimdMathTest.invsqrt (0 ms) 52: [ RUN ] SimdMathTest.maskzInvsqrt 52: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 52: [ RUN ] SimdMathTest.invsqrtPair 52: [ OK ] SimdMathTest.invsqrtPair (0 ms) 52: [ RUN ] SimdMathTest.sqrt 52: [ OK ] SimdMathTest.sqrt (0 ms) 52: [ RUN ] SimdMathTest.sqrtUnsafe 52: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 52: [ RUN ] SimdMathTest.inv 52: [ OK ] SimdMathTest.inv (0 ms) 52: [ RUN ] SimdMathTest.maskzInv 52: [ OK ] SimdMathTest.maskzInv (0 ms) 52: [ RUN ] SimdMathTest.cbrt 52: [ OK ] SimdMathTest.cbrt (0 ms) 52: [ RUN ] SimdMathTest.invcbrt 52: [ OK ] SimdMathTest.invcbrt (0 ms) 52: [ RUN ] SimdMathTest.log2 52: [ OK ] SimdMathTest.log2 (0 ms) 52: [ RUN ] SimdMathTest.log 52: [ OK ] SimdMathTest.log (0 ms) 52: [ RUN ] SimdMathTest.exp2 52: [ OK ] SimdMathTest.exp2 (0 ms) 52: [ RUN ] SimdMathTest.exp2Unsafe 52: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 52: [ RUN ] SimdMathTest.exp 52: [ OK ] SimdMathTest.exp (1 ms) 52: [ RUN ] SimdMathTest.expUnsafe 52: [ OK ] SimdMathTest.expUnsafe (0 ms) 52: [ RUN ] SimdMathTest.pow 52: [ OK ] SimdMathTest.pow (0 ms) 52: [ RUN ] SimdMathTest.powUnsafe 52: [ OK ] SimdMathTest.powUnsafe (0 ms) 52: [ RUN ] SimdMathTest.erf 52: [ OK ] SimdMathTest.erf (0 ms) 52: [ RUN ] SimdMathTest.erfc 52: [ OK ] SimdMathTest.erfc (0 ms) 52: [ RUN ] SimdMathTest.sin 52: [ OK ] SimdMathTest.sin (0 ms) 52: [ RUN ] SimdMathTest.cos 52: [ OK ] SimdMathTest.cos (0 ms) 52: [ RUN ] SimdMathTest.tan 52: [ OK ] SimdMathTest.tan (0 ms) 52: [ RUN ] SimdMathTest.asin 52: [ OK ] SimdMathTest.asin (0 ms) 52: [ RUN ] SimdMathTest.acos 52: [ OK ] SimdMathTest.acos (0 ms) 52: [ RUN ] SimdMathTest.atan 52: [ OK ] SimdMathTest.atan (0 ms) 52: [ RUN ] SimdMathTest.atan2 52: [ OK ] SimdMathTest.atan2 (0 ms) 52: [ RUN ] SimdMathTest.pmeForceCorrection 52: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 52: [ RUN ] SimdMathTest.pmePotentialCorrection 52: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 52: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 52: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 52: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.sqrtSingleAccuracy 52: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 52: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 52: [ RUN ] SimdMathTest.invSingleAccuracy 52: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.cbrtSingleAccuracy 52: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 52: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.log2SingleAccuracy 52: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.logSingleAccuracy 52: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.exp2SingleAccuracy 52: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 52: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 52: [ RUN ] SimdMathTest.expSingleAccuracy 52: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 52: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 52: [ RUN ] SimdMathTest.powSingleAccuracy 52: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 52: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 52: [ RUN ] SimdMathTest.erfSingleAccuracy 52: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.erfcSingleAccuracy 52: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.sinSingleAccuracy 52: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.cosSingleAccuracy 52: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.tanSingleAccuracy 52: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.asinSingleAccuracy 52: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.acosSingleAccuracy 52: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.atanSingleAccuracy 52: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.atan2SingleAccuracy 52: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 52: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 52: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 52: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 52: [----------] 56 tests from SimdMathTest (15 ms total) 52: 52: [----------] 1 test from EmptyArrayRefTest 52: [ RUN ] EmptyArrayRefTest.IsEmpty 52: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 52: [----------] 1 test from EmptyArrayRefTest (0 ms total) 52: 52: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 52: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 52: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 52: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 52: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 52: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 52: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 52: 52: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 52: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 52: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 52: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 52: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 52: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 52: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 52: 52: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 52: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 52: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 52: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 52: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 52: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 52: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 52: 52: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 52: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 52: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 52: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 52: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 52: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 52: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 52: 52: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefReadWriteTest/0.Assignment 52: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 52: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 52: 52: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefReadWriteTest/1.Assignment 52: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 52: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 52: 52: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefArithmeticTest/0.Basic 52: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 52: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 52: 52: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 52: [ RUN ] ArrayRefArithmeticTest/1.Basic 52: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 52: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 52: 52: [----------] 3 tests from SimdVectorOperationsTest 52: [ RUN ] SimdVectorOperationsTest.iprod 52: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 52: [ RUN ] SimdVectorOperationsTest.norm2 52: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 52: [ RUN ] SimdVectorOperationsTest.cprod 52: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 52: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 52: 52: [----------] 32 tests from Simd4FloatingpointTest 52: [ RUN ] Simd4FloatingpointTest.setZero 52: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 52: [ RUN ] Simd4FloatingpointTest.set 52: [ OK ] Simd4FloatingpointTest.set (0 ms) 52: [ RUN ] Simd4FloatingpointTest.add 52: [ OK ] Simd4FloatingpointTest.add (0 ms) 52: [ RUN ] Simd4FloatingpointTest.sub 52: [ OK ] Simd4FloatingpointTest.sub (0 ms) 52: [ RUN ] Simd4FloatingpointTest.mul 52: [ OK ] Simd4FloatingpointTest.mul (0 ms) 52: [ RUN ] Simd4FloatingpointTest.fma 52: [ OK ] Simd4FloatingpointTest.fma (0 ms) 52: [ RUN ] Simd4FloatingpointTest.fms 52: [ OK ] Simd4FloatingpointTest.fms (0 ms) 52: [ RUN ] Simd4FloatingpointTest.fnma 52: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 52: [ RUN ] Simd4FloatingpointTest.fnms 52: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 52: [ RUN ] Simd4FloatingpointTest.abs 52: [ OK ] Simd4FloatingpointTest.abs (0 ms) 52: [ RUN ] Simd4FloatingpointTest.neg 52: [ OK ] Simd4FloatingpointTest.neg (0 ms) 52: [ RUN ] Simd4FloatingpointTest.and 52: [ OK ] Simd4FloatingpointTest.and (0 ms) 52: [ RUN ] Simd4FloatingpointTest.or 52: [ OK ] Simd4FloatingpointTest.or (0 ms) 52: [ RUN ] Simd4FloatingpointTest.xor 52: [ OK ] Simd4FloatingpointTest.xor (0 ms) 52: [ RUN ] Simd4FloatingpointTest.andNot 52: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 52: [ RUN ] Simd4FloatingpointTest.max 52: [ OK ] Simd4FloatingpointTest.max (0 ms) 52: [ RUN ] Simd4FloatingpointTest.min 52: [ OK ] Simd4FloatingpointTest.min (0 ms) 52: [ RUN ] Simd4FloatingpointTest.round 52: [ OK ] Simd4FloatingpointTest.round (0 ms) 52: [ RUN ] Simd4FloatingpointTest.trunc 52: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 52: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 52: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 52: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 52: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 52: [ RUN ] Simd4FloatingpointTest.selectByNotMask 52: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 52: [ RUN ] Simd4FloatingpointTest.cmpNe 52: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 52: [ RUN ] Simd4FloatingpointTest.cmpLe 52: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 52: [ RUN ] Simd4FloatingpointTest.cmpLt 52: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 52: [ RUN ] Simd4FloatingpointTest.andB 52: [ OK ] Simd4FloatingpointTest.andB (0 ms) 52: [ RUN ] Simd4FloatingpointTest.orB 52: [ OK ] Simd4FloatingpointTest.orB (0 ms) 52: [ RUN ] Simd4FloatingpointTest.anyTrue 52: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 52: [ RUN ] Simd4FloatingpointTest.blend 52: [ OK ] Simd4FloatingpointTest.blend (0 ms) 52: [ RUN ] Simd4FloatingpointTest.reduce 52: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 52: [ RUN ] Simd4FloatingpointTest.dotProduct 52: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 52: [ RUN ] Simd4FloatingpointTest.transpose 52: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 52: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 52: 52: [----------] 2 tests from Simd4MathTest 52: [ RUN ] Simd4MathTest.invsqrt 52: [ OK ] Simd4MathTest.invsqrt (0 ms) 52: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 52: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 52: [----------] 2 tests from Simd4MathTest (0 ms total) 52: 52: [----------] 1 test from Simd4VectorOperationsTest 52: [ RUN ] Simd4VectorOperationsTest.norm2 52: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 52: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 288 tests from 22 test suites ran. (16 ms total) 52: [ PASSED ] 288 tests. 52/96 Test #52: SimdUnitTests ................................ Passed 0.09 sec test 53 Start 53: CompatibilityHelpersTests 53: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/compat/tests 53: Test timeout computed to be: 30 53: [==========] Running 9 tests from 6 test suites. 53: [----------] Global test environment set-up. 53: [----------] 4 tests from TemplateMPTest 53: [ RUN ] TemplateMPTest.MpWithIndexInt 53: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 53: [ RUN ] TemplateMPTest.MpWithIndexIntBad 53: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 53: [ RUN ] TemplateMPTest.MpWithIndexBool 53: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 53: [ RUN ] TemplateMPTest.MpWithIndexEnum 53: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 53: [----------] 4 tests from TemplateMPTest (0 ms total) 53: 53: [----------] 1 test from NotNullConstruction 53: [ RUN ] NotNullConstruction.Works 53: [ OK ] NotNullConstruction.Works (0 ms) 53: [----------] 1 test from NotNullConstruction (0 ms total) 53: 53: [----------] 1 test from NotNullCasting 53: [ RUN ] NotNullCasting.Works 53: [ OK ] NotNullCasting.Works (0 ms) 53: [----------] 1 test from NotNullCasting (0 ms total) 53: 53: [----------] 1 test from NotNullAssignment 53: [ RUN ] NotNullAssignment.Works 53: [ OK ] NotNullAssignment.Works (0 ms) 53: [----------] 1 test from NotNullAssignment (0 ms total) 53: 53: [----------] 1 test from MakeNotNull 53: [ RUN ] MakeNotNull.Works 53: [ OK ] MakeNotNull.Works (0 ms) 53: [----------] 1 test from MakeNotNull (0 ms total) 53: 53: [----------] 1 test from NotNull 53: [ RUN ] NotNull.WorksInContainers 53: [ OK ] NotNull.WorksInContainers (0 ms) 53: [----------] 1 test from NotNull (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 9 tests from 6 test suites ran. (0 ms total) 53: [ PASSED ] 9 tests. 53/96 Test #53: CompatibilityHelpersTests .................... Passed 0.07 sec test 54 Start 54: GmxAnaTest 54: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxAnaTest.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxana/tests 54: Test timeout computed to be: 600 54: [==========] Running 31 tests from 4 test suites. 54: [----------] Global test environment set-up. 54: [----------] 7 tests from Entropy 54: [ RUN ] Entropy.Schlitter_300_NoLinear 54: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 54: [ RUN ] Entropy.Schlitter_300_Linear 54: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 54: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 54: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 54: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 54: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 54: [ RUN ] Entropy.QuasiHarmonic_200_Linear 54: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 54: [ RUN ] Entropy.EntropyCompare_200_Linear 54: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 54: [ RUN ] Entropy.EntropyCompare_300_Linear 54: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 54: [----------] 7 tests from Entropy (0 ms total) 54: 54: [----------] 2 tests from GmxChiTest 54: [ RUN ] GmxChiTest.gmxchiWorksWithAll 54: Analyzing from residue 1 to residue 11 54: 10 residues with dihedrals found 54: 46 dihedrals found 54: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 54: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 54: j after resetting (nr. active dihedrals) = 46 54: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 54: Now calculating transitions... 54: Total number of transitions: 0 54: Now printing out transitions and OPs... 54: Now printing out rotamer occupancies... 54: Now calculating Chi product trajectories... 54: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 54: [ OK ] GmxChiTest.gmxchiWorksWithAll (399 ms) 54: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 54: Analyzing from residue 2 to residue 6 54: 5 residues with dihedrals found 54: 23 dihedrals found 54: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 54: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 54: j after resetting (nr. active dihedrals) = 23 54: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 54: Now calculating transitions... 54: Total number of transitions: 0 54: Now printing out transitions and OPs... 54: Now printing out rotamer occupancies... 54: Now calculating Chi product trajectories... 54: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 54: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (200 ms) 54: [----------] 2 tests from GmxChiTest (670 ms total) 54: 54: [----------] 10 tests from MindistTest 54: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 0: 'atom1' 54: Selected 1: 'atom2' 54: [ OK ] MindistTest.mindistWorksWithSingleAtoms (5 ms) 54: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 2: 'atom3' 54: Selected 3: 'atoms12' 54: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 54: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 0: 'atom1' 54: Selected 1: 'atom2' 54: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 54: [ RUN ] MindistTest.mindistPicksUpContacts 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 0: 'atom1' 54: Selected 1: 'atom2' 54: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 54: [ RUN ] MindistTest.ngWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 0: 'atom1' 54: Selected 1: 'atom2' 54: Selected 2: 'atom3' 54: [ OK ] MindistTest.ngWorks (0 ms) 54: [ RUN ] MindistTest.groupWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 3: 'atoms12' 54: Selected 2: 'atom3' 54: [ OK ] MindistTest.groupWorks (0 ms) 54: [ RUN ] MindistTest.maxDistWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 2: 'atom3' 54: Selected 3: 'atoms12' 54: [ OK ] MindistTest.maxDistWorks (0 ms) 54: [ RUN ] MindistTest.noPbcWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 0: 'atom1' 54: Selected 1: 'atom2' 54: [ OK ] MindistTest.noPbcWorks (0 ms) 54: [ RUN ] MindistTest.resPerTimeWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 3: 'atoms12' 54: Selected 2: 'atom3' 54: [ OK ] MindistTest.resPerTimeWorks (0 ms) 54: [ RUN ] MindistTest.matrixWorks 54: Group 0 ( atom1) has 1 elements 54: Group 1 ( atom2) has 1 elements 54: Group 2 ( atom3) has 1 elements 54: Group 3 ( atoms12) has 2 elements 54: Group 4 ( atoms23) has 2 elements 54: Group 5 ( atoms123) has 3 elements 54: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 54: Reading frame 0 time 0.000 Last frame 0 time 0.000 54: Selected 5: 'atoms123' 54: Special case: making distance matrix between all atoms in group atoms123 54: [ OK ] MindistTest.matrixWorks (0 ms) 54: [----------] 10 tests from MindistTest (9 ms total) 54: 54: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: trr version: GMX_trn_file (single precision) 54: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 54: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 54: Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (0 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 54: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 54: Group 0 ( System) has 6 elements 54: Group 1 ( Water) has 6 elements 54: Group 2 ( SOL) has 6 elements 54: Select a group: Reading frame 0 time 0.000 54: WARNING: If there are molecules in the input trajectory file 54: that are broken across periodic boundaries, they 54: cannot be made whole (or treated as whole) without 54: you providing a run input file. 54: 54: Reading frame 1 time 1.000 Last frame 1 time 1.000 54: 54: WARNING: Masses and atomic (Van der Waals) radii will be guessed 54: based on residue and atom names, since they could not be 54: definitively assigned from the information in your input 54: files. These guessed numbers might deviate from the mass 54: and radius of the atom type. Please check the output 54: files if necessary. Note, that this functionality may 54: be removed in a future GROMACS version. Please, consider 54: using another file format for your input. 54: 54: Selected 0: 'System' 54: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 54: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (11 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 31 tests from 4 test suites ran. (692 ms total) 54: [ PASSED ] 31 tests. 54/96 Test #54: GmxAnaTest ................................... Passed 0.77 sec test 55 Start 55: GmxPreprocessTests 55: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 260 tests from 16 test suites. 55: [----------] Global test environment set-up. 55: [----------] 1 test from ConvertInteractionsTest 55: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 55: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 55: [----------] 1 test from ConvertInteractionsTest (0 ms total) 55: 55: [----------] 4 tests from GenconfTest 55: [ RUN ] GenconfTest.nbox_Works 55: [ OK ] GenconfTest.nbox_Works (0 ms) 55: [ RUN ] GenconfTest.nbox_norenumber_Works 55: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 55: [ RUN ] GenconfTest.nbox_dist_Works 55: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 55: [ RUN ] GenconfTest.nbox_rot_Works 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: center of geometry: 1.733667, 1.477000, 0.905167 55: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 55: [----------] 4 tests from GenconfTest (1 ms total) 55: 55: [----------] 2 tests from GenionTest 55: [ RUN ] GenionTest.HighConcentrationIonPlacement 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 55: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 55: buffer. The cluster pair list does have a buffering effect, but choosing 55: a larger rlist might be necessary for good energy conservation. 55: 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 55: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 55: < 0 55: 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: Number of degrees of freedom in T-Coupling group rest is 1308.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 NOTEs 55: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 55: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 55: Group 0 ( System) has 653 elements 55: Group 1 ( Water) has 648 elements 55: Group 2 ( SOL) has 648 elements 55: Group 3 ( non-Water) has 5 elements 55: Group 4 ( Other) has 5 elements 55: Group 5 ( METH) has 5 elements 55: Select a group: Number of (3-atomic) solvent molecules: 216 55: Using random seed 1997. 55: Replacing solvent molecule 56 (atom 168) with NA 55: Replacing solvent molecule 120 (atom 360) with NA 55: Replacing solvent molecule 182 (atom 546) with NA 55: Replacing solvent molecule 71 (atom 213) with NA 55: Replacing solvent molecule 189 (atom 567) with CL 55: Replacing solvent molecule 54 (atom 162) with CL 55: Replacing solvent molecule 155 (atom 465) with CL 55: Replacing solvent molecule 99 (atom 297) with CL 55: 55: Setting the LD random seed to 2007922231 55: 55: Generated 331705 of the 331705 non-bonded parameter combinations 55: 55: Generated 331705 of the 331705 1-4 parameter combinations 55: 55: Excluding 2 bonded neighbours molecule type 'SOL' 55: 55: Excluding 3 bonded neighbours molecule type 'methane' 55: 55: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 55: Analysing residue names: 55: There are: 216 Water residues 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: This run will generate roughly 0 Mb of data 55: Will try to add 4 NA ions and 4 CL ions. 55: Select a continuous group of solvent molecules 55: Selected 1: 'Water' 55: [ OK ] GenionTest.HighConcentrationIonPlacement (161 ms) 55: [ RUN ] GenionTest.NoIonPlacement 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 55: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 55: buffer. The cluster pair list does have a buffering effect, but choosing 55: a larger rlist might be necessary for good energy conservation. 55: 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 55: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 55: < 0 55: 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: Number of degrees of freedom in T-Coupling group rest is 1308.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 NOTEs 55: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 55: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 55: No ions to add, will just copy input configuration. 55: Setting the LD random seed to 534281962 55: 55: Generated 331705 of the 331705 non-bonded parameter combinations 55: 55: Generated 331705 of the 331705 1-4 parameter combinations 55: 55: Excluding 2 bonded neighbours molecule type 'SOL' 55: 55: Excluding 3 bonded neighbours molecule type 'methane' 55: 55: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216_with_methane.gro' 55: Analysing residue names: 55: There are: 216 Water residues 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] GenionTest.NoIonPlacement (150 ms) 55: [----------] 2 tests from GenionTest (311 ms total) 55: 55: [----------] 1 test from GenRestrTest 55: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 55: 55: Reading structure file 55: Group 0 ( System) has 156 elements 55: Group 1 ( Protein) has 156 elements 55: Group 2 ( Protein-H) has 75 elements 55: Group 3 ( C-alpha) has 10 elements 55: Group 4 ( Backbone) has 30 elements 55: Group 5 ( MainChain) has 40 elements 55: Group 6 ( MainChain+Cb) has 49 elements 55: Group 7 ( MainChain+H) has 52 elements 55: Group 8 ( SideChain) has 104 elements 55: Group 9 ( SideChain-H) has 35 elements 55: Select a group: Select group to position restrain 55: Selected 3: 'C-alpha' 55: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 55: [----------] 1 test from GenRestrTest (1 ms total) 55: 55: [----------] 9 tests from PreprocessingAtomTypesTest 55: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 55: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 55: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 55: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 55: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 55: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 55: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 55: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 55: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 55: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 55: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 55: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 55: 55: [----------] 10 tests from PreprocessingBondAtomTypeTest 55: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 55: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 55: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 55: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 55: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 55: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 55: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 55: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 55: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 55: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 55: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 55: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 55: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 55: 55: [----------] 3 tests from GromppDirectiveTest 55: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives.top, line 59]: 55: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 9.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 55: Setting the LD random seed to 1207959469 55: 55: Generated 10 of the 10 non-bonded parameter combinations 55: 55: Generated 10 of the 10 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -143220770 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 55: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives.top, line 59]: 55: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 55: coefficients that do not sum to zero. This does not affect the simulation 55: and can be ignored, unless you are comparing potential energy values with 55: other force field ports and/or MD software. 55: First such dihedral in molecule A, involving atoms 0 2 1 3 55: 55: 55: NOTE 2 [file directives.top, line 59]: 55: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 9.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 3 NOTEs 55: Setting the LD random seed to -1362141701 55: 55: Generated 10 of the 10 non-bonded parameter combinations 55: 55: Generated 10 of the 10 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -539329622 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (2 ms) 55: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 55: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (0 ms) 55: [----------] 3 tests from GromppDirectiveTest (5 ms total) 55: 55: [----------] 6 tests from InsertMoleculesTest 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 55: Reading solute configuration 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Try 1 success (now 8 atoms)! 55: 55: Added 1 molecules (out of 1 requested) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 55: 55: Output configuration contains 8 atoms in 4 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (0 ms) 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Try 1 success (now 2 atoms)! 55: Try 2 success (now 4 atoms)! 55: Try 3 success (now 6 atoms)! 55: Try 4 success (now 8 atoms)! 55: Try 5 success (now 10 atoms)! 55: 55: Added 5 molecules (out of 5 requested) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 55: 55: Output configuration contains 10 atoms in 10 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Try 1 success (now 2 atoms)! 55: Try 2 success (now 4 atoms)! 55: Try 3 success (now 6 atoms)! 55: Try 4 success (now 8 atoms)! 55: Try 5 success (now 10 atoms)! 55: 55: Added 5 molecules (out of 5 requested) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 55: 55: Output configuration contains 10 atoms in 10 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 55: Reading solute configuration 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Try 1 success (now 8 atoms)! 55: Try 2 success (now 10 atoms)! 55: 55: Added 2 molecules (out of 2 requested) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 55: 55: Output configuration contains 10 atoms in 4 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 55: Reading solute configuration 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Try 1 success (now 650 atoms)! 55: Try 2 success (now 652 atoms)! 55: Try 3 success (now 654 atoms)! 55: Try 4 success (now 656 atoms)! 55: 55: Added 4 molecules (out of 4 requested) 55: Replaced 8 residues (24 atoms) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 55: 55: Output configuration contains 632 atoms in 212 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 55: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Using random seed 1997 55: Read 4 positions from file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 55: 55: Try 1 success (now 2 atoms)! 55: Try 2 success (now 4 atoms)! 55: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 55: Try 13 success (now 6 atoms)! 55: 55: Added 3 molecules (out of 4 requested) 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 55: 55: Output configuration contains 6 atoms in 3 residues 55: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 55: [----------] 6 tests from InsertMoleculesTest (6 ms total) 55: 55: [----------] 3 tests from MassRepartitioning 55: [ RUN ] MassRepartitioning.ValidCaseWorks 55: The smallest mass in the system is 2, setting the minimum mass to 6 55: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 55: [ RUN ] MassRepartitioning.UnboundGivesWarning 55: 55: WARNING 1 [file unknown]: 55: The are 1 atoms that have a mass below the mass repartitioning limit but 55: are not bound. These masses cannot be repartitioned. 55: 55: The smallest mass in the system is 2, setting the minimum mass to 6 55: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 55: [ RUN ] MassRepartitioning.LightPartnerGivesError 55: 55: ERROR 1 [file unknown]: 55: Light atoms are bound to at least one atom that has a too low mass for 55: repartitioning 55: 55: The smallest mass in the system is 2, setting the minimum mass to 6 55: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 55: [----------] 3 tests from MassRepartitioning (0 ms total) 55: 55: [----------] 35 tests from GetIrTest 55: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 55: Ignoring obsolete mdp entry 'title' 55: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (1 ms) 55: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 55: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 55: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 55: [ RUN ] GetIrTest.RejectsValueWithoutKey 55: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 55: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 55: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 55: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 55: [ RUN ] GetIrTest.AcceptsEmptyLines 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 55: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 55: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 55: [ RUN ] GetIrTest.MtsCheckNstenergy 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 55: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 55: Setting nstcalcenergy (100) equal to nstenergy (5) 55: 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 55: [ RUN ] GetIrTest.MtsCheckNstpcouple 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 55: Pressure coupling incorrect number of values (I need exactly 1) 55: 55: 55: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 55: Pressure coupling incorrect number of values (I need exactly 1) 55: 55: 55: ERROR 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 55: With multiple time stepping, nstpcouple should be a multiple of 55: mts-factor 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: 55: ERROR 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 55: The Berendsen barostat does not generate any strictly correct ensemble, 55: and should not be used for new production simulations (in our opinion). 55: We recommend using the C-rescale barostat instead. 55: 55: 55: ERROR 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 55: compressibility must be > 0 when using pressure coupling Berendsen 55: 55: 55: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 55: [ RUN ] GetIrTest.MtsCheckNstdhdl 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 55: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 55: Setting nstcalcenergy (100) equal to nstdhdl (5) 55: 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: 55: ERROR 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 55: Lambda state must be set, either with init-lambda-state or with 55: init-lambda 55: 55: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 55: [ RUN ] GetIrTest.MtsCheckSDNotSupported 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 55: Multiple time stepping is only supported with integrator md 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 55: [ RUN ] GetIrTest.AcceptsElectricField 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 55: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 55: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 55: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 55: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 55: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 55: [ RUN ] GetIrTest.RejectsImplicitSolventYes 55: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 55: [ RUN ] GetIrTest.AcceptsMimic 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsMimic (2 ms) 55: [ RUN ] GetIrTest.AcceptsTransformationCoord 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 55: pull-coord2 has a non-zero force constant and is also referenced in 55: pull-coord1-expression. Make sure that this is intended. In most use 55: cases, the pull coordinates referenced by a transformation coordinate 55: should have their force constant set to zero. 55: 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 55: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 55: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 55: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 55: pull-coord2 can not use pull-coord1 in the transformation since this is a 55: constraint 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 55: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 55: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 55: 'transformation' 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 55: [ RUN ] GetIrTest.MissingTransformationCoordExpression 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 55: pull-coord1-expression not set for pull coordinate of geometry 55: 'transformation' 55: 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 55: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 55: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 55: in total 100001 steps. This is not compatible with using soft-core 55: potentials. 55: 55: 55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 55: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 55: won't change anymore after step 100000 until the end of the simulation 55: after 100001 steps. 55: 55: 55: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 55: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 55: won't change anymore after step 100000 until the end of the simulation 55: after 100001 steps. 55: 55: 55: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 55: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 55: components won't change anymore after step 100000 until the end of the 55: simulation after 100001 steps. 55: 55: 55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 55: 55: ERROR 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 55: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 55: components won't change anymore after step 100000 until the end of the 55: simulation after 100001 steps. 55: 55: 55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 55: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 55: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 55: [----------] 35 tests from GetIrTest (47 ms total) 55: 55: [----------] 6 tests from SolvateTest 55: [ RUN ] SolvateTest.cs_box_Works 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 1x1x1 boxes 55: Solvent box contains 270 atoms in 90 residues 55: Removed 129 solvent atoms due to solvent-solvent overlap 55: Sorting configuration 55: Found 1 molecule type: 55: SOL ( 3 atoms): 47 residues 55: Generated solvent containing 141 atoms in 47 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 55: 55: Output configuration contains 141 atoms in 47 residues 55: Volume : 1.331 (nm^3) 55: Density : 1056.36 (g/l) 55: Number of solvent molecules: 47 55: 55: [ OK ] SolvateTest.cs_box_Works (2 ms) 55: [ RUN ] SolvateTest.cs_cp_Works 55: Reading solute configuration 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 2x2x2 boxes 55: Solvent box contains 3660 atoms in 1220 residues 55: Removed 987 solvent atoms due to solvent-solvent overlap 55: Removed 15 solvent atoms due to solute-solvent overlap 55: Sorting configuration 55: Found 1 molecule type: 55: SOL ( 3 atoms): 886 residues 55: Generated solvent containing 2658 atoms in 886 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 55: 55: Output configuration contains 2664 atoms in 888 residues 55: Volume : 27.2709 (nm^3) 55: Density : 974.777 (g/l) 55: Number of solvent molecules: 886 55: 55: [ OK ] SolvateTest.cs_cp_Works (11 ms) 55: [ RUN ] SolvateTest.cs_cp_p_Works 55: Reading solute configuration 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 2x2x2 boxes 55: Solvent box contains 3660 atoms in 1220 residues 55: Removed 987 solvent atoms due to solvent-solvent overlap 55: Removed 15 solvent atoms due to solute-solvent overlap 55: Sorting configuration 55: Found 1 molecule type: 55: SOL ( 3 atoms): 886 residues 55: Generated solvent containing 2658 atoms in 886 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 55: 55: Output configuration contains 2664 atoms in 888 residues 55: Volume : 27.2709 (nm^3) 55: Density : 974.777 (g/l) 55: Number of solvent molecules: 886 55: 55: Processing topology 55: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 55: [ OK ] SolvateTest.cs_cp_p_Works (11 ms) 55: [ RUN ] SolvateTest.shell_Works 55: Reading solute configuration 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 2x2x2 boxes 55: Solvent box contains 3660 atoms in 1220 residues 55: Removed 987 solvent atoms due to solvent-solvent overlap 55: Removed 1902 solvent atoms more than 1.000000 nm from solute. 55: Removed 15 solvent atoms due to solute-solvent overlap 55: Sorting configuration 55: Found 1 molecule type: 55: SOL ( 3 atoms): 252 residues 55: Generated solvent containing 756 atoms in 252 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 55: 55: Output configuration contains 762 atoms in 254 residues 55: Volume : 27.2709 (nm^3) 55: Density : 279.3 (g/l) 55: Number of solvent molecules: 252 55: 55: [ OK ] SolvateTest.shell_Works (6 ms) 55: [ RUN ] SolvateTest.update_Topology_Works 55: Reading solute configuration 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 3x3x3 boxes 55: Solvent box contains 14952 atoms in 4984 residues 55: Removed 2787 solvent atoms due to solvent-solvent overlap 55: Removed 30 solvent atoms due to solute-solvent overlap 55: Sorting configuration 55: Found 2 different molecule types: 55: HOH ( 3 atoms): 1876 residues 55: SOL ( 3 atoms): 2169 residues 55: Generated solvent containing 0 atoms in 0 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 55: 55: Output configuration contains 12141 atoms in 4047 residues 55: Volume : 125 (nm^3) 55: Density : 968.963 (g/l) 55: Number of solvent molecules: 4045 55: 55: Processing topology 55: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 55: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 55: [ OK ] SolvateTest.update_Topology_Works (44 ms) 55: [ RUN ] SolvateTest.cs_pdb_big_box_Works 55: Reading solvent configuration 55: 55: Initialising inter-atomic distances... 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 55: from the source below. This means the results may be different 55: compared to previous GROMACS versions. 55: 55: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 55: A. Bondi 55: van der Waals Volumes and Radii 55: J. Phys. Chem. (1964) 55: DOI: 10.1021/j100785a001 55: -------- -------- --- Thank You --- -------- -------- 55: 55: Generating solvent configuration 55: Will generate new solvent configuration of 2x2x2 boxes 55: Solvent box contains 1218 atoms in 406 residues 55: Removed 555 solvent atoms due to solvent-solvent overlap 55: Sorting configuration 55: Found 1 molecule type: 55: SOL ( 3 atoms): 221 residues 55: Generated solvent containing 663 atoms in 221 residues 55: Writing generated configuration to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 55: 55: Output configuration contains 663 atoms in 221 residues 55: Volume : 8 (nm^3) 55: Density : 826.409 (g/l) 55: Number of solvent molecules: 221 55: 55: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 55: [----------] 6 tests from SolvateTest (79 ms total) 55: 55: [----------] 1 test from TopDirTests 55: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 55: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 55: [----------] 1 test from TopDirTests (0 ms total) 55: 55: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 55: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 55: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 55: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 55: Skipping interaction type that does not represent a interaction with parameters converted in grompp 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 55: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (0 ms total) 55: 55: [----------] 45 tests from SinglePeptideFragments/EditconfTest 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 55: 55: Select a group for output: 55: Group 0 ( two_residues) has 23 elements 55: There is one group in the index 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : 0.212 1.187 3.527 (nm) 55: new center : 4.028 2.819 3.723 (nm) 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.42 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.42 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.42 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: shift : -0.814 1.104 2.657 (nm) 55: new center : 3.002 2.736 2.852 (nm) 55: new box vectors : 6.004 5.472 5.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 187.40 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.28 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.28 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.28 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (2 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (0 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 55: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 55: Note that major changes are planned in future for editconf, to improve usability and utility. 55: Read 252 atoms 55: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 55: No velocities found 55: system size : 2.004 1.472 1.704 (nm) 55: center : 3.816 1.632 0.195 (nm) 55: box vectors : 8.056 5.637 7.445 (nm) 55: box angles : 90.00 90.00 90.00 (degrees) 55: box volume : 338.10 (nm^3) 55: new center : 3.816 1.632 0.195 (nm) 55: new box vectors : 5.004 4.472 4.704 (nm) 55: new box angles : 90.00 90.00 90.00 (degrees) 55: new box volume : 105.27 (nm^3) 55: 55: WARNING: No boxtype specified - distance condition applied in each dimension. 55: If the molecule rotates the actual distance will be smaller. You might want 55: to use a cubic box instead, or why not try a dodecahedron today? 55: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) 55: [----------] 45 tests from SinglePeptideFragments/EditconfTest (62 ms total) 55: 55: [----------] 16 tests from CorrectVelocity/MaxwellTest 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 55: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 55: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 55: [----------] 16 tests from CorrectVelocity/MaxwellTest (8 ms total) 55: 55: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to -50370561 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -1384705 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to -8552705 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to 1585424959 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to -676922437 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to 1809225693 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to 2147440091 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -1644503562 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to 1073527277 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to 1659535098 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to -1413619905 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -4260364 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (0 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 55: Ignoring obsolete mdp entry 'title' 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 1 [file directives-cmap.top, line 114]: 55: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 55: any other atom in the same moleculetype. Although technically this might 55: not cause issues in a simulation, this often means that the user forgot 55: to add a bond/potential/constraint or put multiple molecules in the same 55: moleculetype definition by mistake. Run with -v to get information for 55: each atom. 55: 55: Number of degrees of freedom in T-Coupling group rest is 12.00 55: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 55: 55: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 55: NVE simulation: will use the initial temperature of 300.000 K for 55: determining the Verlet buffer size 55: 55: 55: There were 2 NOTEs 55: Setting the LD random seed to -735327697 55: 55: Generated 3 of the 3 non-bonded parameter combinations 55: 55: Generated 3 of the 3 1-4 parameter combinations 55: 55: Excluding 0 bonded neighbours molecule type 'A' 55: 55: Setting gen_seed to -1142624801 55: 55: Velocities were taken from a Maxwell distribution at 300 K 55: Analysing residue names: 55: There are: 1 Other residues 55: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 55: 55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 55: 55: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 55: 55: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 55: 55: Note that mdrun will redetermine rlist based on the actual pair-list setup 55: 55: This run will generate roughly 0 Mb of data 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (2 ms) 55: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 55: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (0 ms) 55: [----------] 23 tests from CMAPDefinesAndErrors/GromppDirectiveTest (19 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 260 tests from 16 test suites ran. (545 ms total) 55: [ PASSED ] 220 tests. 55: [ SKIPPED ] 40 tests, listed below: 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 55: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 55/96 Test #55: GmxPreprocessTests ........................... Passed 0.62 sec test 56 Start 56: Pdb2gmx1Test 56: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 30 tests from 1 test suite. 56: [----------] Global test environment set-up. 56: [----------] 30 tests from Oplsaa/Pdb2gmxTest 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (19 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (16 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 663 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.112 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 778 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.357 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 696 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.128 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (18 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: PRO-COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 618 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.883 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (17 ms) 56: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/oplsaa.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Oplsaa force field in directory oplsaa.ff 56: 56: going to rename oplsaa.ff/aminoacids.r2b 56: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Oplsaa) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2524 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.578 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Oplsaa force field and the tip5p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (54 ms) 56: [----------] 30 tests from Oplsaa/Pdb2gmxTest (754 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 30 tests from 1 test suite ran. (754 ms total) 56: [ PASSED ] 30 tests. 56/96 Test #56: Pdb2gmx1Test ................................. Passed 0.84 sec test 57 Start 57: Pdb2gmx2Test 57: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests 57: Test timeout computed to be: 1920 57: [==========] Running 40 tests from 2 test suites. 57: [----------] Global test environment set-up. 57: [----------] 20 tests from G43a1/Pdb2gmxTest 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 305 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 165 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 172, now 167 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 77 impropers, 241 angles 57: 267 pairs, 167 bonds and 0 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 429 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 202 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 216, now 211 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 134 impropers, 316 angles 57: 273 pairs, 211 bonds and 0 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 349 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 168 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 179, now 174 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 102 impropers, 260 angles 57: 242 pairs, 174 bonds and 0 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 299 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 150 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 159, now 154 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 80 impropers, 227 angles 57: 232 pairs, 154 bonds and 0 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1256 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 635 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 655, now 650 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 350 impropers, 955 angles 57: 972 pairs, 650 bonds and 0 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (37 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 37 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 305 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 165 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 172, now 167 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 77 impropers, 241 angles 57: 267 pairs, 167 bonds and 37 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 53 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 429 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 202 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 216, now 211 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 134 impropers, 316 angles 57: 273 pairs, 211 bonds and 51 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 36 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 349 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 168 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 179, now 174 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 102 impropers, 260 angles 57: 242 pairs, 174 bonds and 36 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 33 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 299 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 150 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 159, now 154 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 80 impropers, 227 angles 57: 232 pairs, 154 bonds and 31 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 146 virtual sites 57: Added 10 dummy masses 57: Added 29 new constraints 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1256 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 635 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 655, now 650 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 350 impropers, 955 angles 57: 972 pairs, 650 bonds and 137 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos43a1 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 305 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 165 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 172, now 167 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 77 impropers, 241 angles 57: 267 pairs, 167 bonds and 0 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 429 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 202 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 216, now 211 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 134 impropers, 316 angles 57: 273 pairs, 211 bonds and 0 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (20 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 349 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 168 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 179, now 174 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 102 impropers, 260 angles 57: 242 pairs, 174 bonds and 0 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 299 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 150 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 159, now 154 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 80 impropers, 227 angles 57: 232 pairs, 154 bonds and 0 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1256 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 635 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 655, now 650 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 350 impropers, 955 angles 57: 972 pairs, 650 bonds and 0 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (36 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 37 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 305 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 165 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 172, now 167 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 77 impropers, 241 angles 57: 267 pairs, 167 bonds and 37 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 53 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 429 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 202 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 216, now 211 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 134 impropers, 316 angles 57: 273 pairs, 211 bonds and 51 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 36 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 349 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 168 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 179, now 174 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 102 impropers, 260 angles 57: 242 pairs, 174 bonds and 36 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 33 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 299 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 150 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 159, now 154 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 80 impropers, 227 angles 57: 232 pairs, 154 bonds and 31 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge 0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 57: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.rtp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos43a1.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 146 virtual sites 57: Added 10 dummy masses 57: Added 29 new constraints 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1256 dihedrals 57: Using the Gromos43a1 force field in directory gromos43a1.ff 57: 57: going to rename gromos43a1.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos43a1) 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 635 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 655, now 650 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 350 impropers, 955 angles 57: 972 pairs, 650 bonds and 137 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos43a1 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (38 ms) 57: [----------] 20 tests from G43a1/Pdb2gmxTest (471 ms total) 57: 57: [----------] 20 tests from G53a6/Pdb2gmxTest 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 312 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 167 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 174, now 169 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 79 impropers, 245 angles 57: 267 pairs, 169 bonds and 0 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 443 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 206 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 220, now 215 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 138 impropers, 324 angles 57: 273 pairs, 215 bonds and 0 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 356 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 170 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 181, now 176 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 104 impropers, 264 angles 57: 242 pairs, 176 bonds and 0 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 306 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 152 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 161, now 156 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 82 impropers, 231 angles 57: 232 pairs, 156 bonds and 0 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1270 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 639 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 659, now 654 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 354 impropers, 963 angles 57: 972 pairs, 654 bonds and 0 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 39 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 312 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 167 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 174, now 169 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 79 impropers, 245 angles 57: 267 pairs, 169 bonds and 39 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 57 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 443 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 206 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 220, now 215 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 138 impropers, 324 angles 57: 273 pairs, 215 bonds and 55 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 38 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 356 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 170 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 181, now 176 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 104 impropers, 264 angles 57: 242 pairs, 176 bonds and 38 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 35 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 306 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 152 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 161, now 156 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 82 impropers, 231 angles 57: 232 pairs, 156 bonds and 33 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 150 virtual sites 57: Added 10 dummy masses 57: Added 29 new constraints 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1270 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 639 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 659, now 654 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 354 impropers, 963 angles 57: 972 pairs, 654 bonds and 141 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos53a6 force field and the spc water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 312 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 167 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 174, now 169 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 79 impropers, 245 angles 57: 267 pairs, 169 bonds and 0 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 443 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 206 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 220, now 215 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 138 impropers, 324 angles 57: 273 pairs, 215 bonds and 0 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 356 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 170 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 181, now 176 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 104 impropers, 264 angles 57: 242 pairs, 176 bonds and 0 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 306 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 152 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 161, now 156 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 82 impropers, 231 angles 57: 232 pairs, 156 bonds and 0 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1270 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 639 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 659, now 654 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 354 impropers, 963 angles 57: 972 pairs, 654 bonds and 0 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (39 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 25 donors and 23 acceptors were found. 57: There are 41 hydrogen bonds 57: Will use HISE for residue 8 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS3 HIS8 57: SG9 NE251 57: HIS8 NE251 1.055 57: MET12 SD83 0.763 0.990 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 39 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 267 pairs 57: Before cleaning: 312 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 57: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 128 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (128 atoms, 16 residues) 57: 57: Identified residue ALA2 as a starting terminus. 57: 57: Identified residue SER17 as a ending terminus. 57: Start terminus ALA-2: NH3+ 57: End terminus SER-17: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 167 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 174, now 169 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 90 dihedrals, 79 impropers, 245 angles 57: 267 pairs, 169 bonds and 39 virtual sites 57: 57: Total mass 1846.116 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 30 donors and 22 acceptors were found. 57: There are 36 hydrogen bonds 57: Will use HISE for residue 29 57: Will use HISE for residue 32 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS27 HIS29 57: SG90 NE2111 57: HIS29 NE2111 0.987 57: HIS32 NE2135 1.590 1.155 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 57 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 273 pairs 57: Before cleaning: 443 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 57: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 149 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (149 atoms, 16 residues) 57: 57: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue THR18 as a starting terminus. 57: 57: Identified residue PHE33 as a ending terminus. 57: Start terminus THR-18: NH3+ 57: End terminus PHE-33: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 206 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 220, now 215 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 93 dihedrals, 138 impropers, 324 angles 57: 273 pairs, 215 bonds and 55 virtual sites 57: 57: Total mass 2088.361 a.m.u. 57: 57: Total charge 1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 22 acceptors were found. 57: There are 26 hydrogen bonds 57: Will use HISE for residue 45 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS45 57: NE295 57: MET46 SD102 1.078 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 38 virtual sites 57: Added 4 dummy masses 57: Added 8 new constraints 57: 57: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 242 pairs 57: Before cleaning: 356 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 57: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 132 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (132 atoms, 16 residues) 57: 57: Identified residue ALA34 as a starting terminus. 57: 57: Identified residue ALA49 as a ending terminus. 57: Start terminus ALA-34: NH3+ 57: End terminus ALA-49: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 170 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 181, now 176 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 81 dihedrals, 104 impropers, 264 angles 57: 242 pairs, 176 bonds and 38 virtual sites 57: 57: Total mass 1861.132 a.m.u. 57: 57: Total charge -1.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 22 donors and 21 acceptors were found. 57: There are 30 hydrogen bonds 57: Will use HISE for residue 60 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: HIS60 57: NE285 57: CYS62 SG98 0.803 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 35 virtual sites 57: Added 4 dummy masses 57: Added 10 new constraints 57: 57: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 232 pairs 57: Before cleaning: 306 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 57: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 57: 57: chain #res #atoms 57: 57: 1 ' ' 16 117 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 (117 atoms, 16 residues) 57: 57: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 57: 57: Identified residue LYS50 as a starting terminus. 57: 57: Identified residue PRO65 as a ending terminus. 57: Start terminus LYS-50: NH3+ 57: End terminus PRO-65: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 16 residues with 152 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 161, now 156 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 78 dihedrals, 82 impropers, 231 angles 57: 232 pairs, 156 bonds and 33 virtual sites 57: 57: Total mass 1662.887 a.m.u. 57: 57: Total charge -0.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 57: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.r2b 57: All occupancies are one 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/atomtypes.atp 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.rtp 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.hdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.n.tdb 57: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/gromos53a6.ff/aminoacids.c.tdb 57: Analysing hydrogen-bonding network for automated assignment of histidine 57: protonation. 89 donors and 98 acceptors were found. 57: There are 129 hydrogen bonds 57: Will use HISE for residue 31 57: Will use HISE for residue 51 57: 9 out of 9 lines of specbond.dat converted successfully 57: Special Atom Distance matrix: 57: CYS25 HIS31 HIS51 57: SG14 NE264 NE2226 57: HIS31 NE264 1.921 57: HIS51 NE2226 1.498 2.650 57: CYS80 SG477 0.207 1.984 1.570 57: Linking CYS-25 SG-14 and CYS-80 SG-477... 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: 57: WARNING: Duplicate line found in or between hackblock and rtp entries 57: 57: Marked 150 virtual sites 57: Added 10 dummy masses 57: Added 29 new constraints 57: 57: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom H used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: 57: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 57: to an entry in the topology database, but the atom O used in 57: an interaction of type angle in that entry is not found in the 57: input file. Perhaps your atom and/or residue naming needs to be 57: fixed. 57: 57: 57: Before cleaning: 972 pairs 57: Before cleaning: 1270 dihedrals 57: Using the Gromos53a6 force field in directory gromos53a6.ff 57: 57: going to rename gromos53a6.ff/aminoacids.r2b 57: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 57: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 57: 57: Analyzing pdb file 57: Splitting chemical chains based on TER records or chain id changing. 57: 57: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 57: 57: chain #res #atoms 57: 57: 1 'A' 58 488 57: 57: All occupancies are one 57: 57: Reading residue database... (Gromos53a6) 57: 57: Using default: not generating all possible dihedrals 57: 57: Using default: excluding 3 bonded neighbors 57: 57: Using default: generating 1,4 H--H interactions 57: 57: Using default: removing proper dihedrals found on the same bond as a proper dihedral 57: 57: Processing chain 1 'A' (488 atoms, 58 residues) 57: 57: Identified residue ASN24 as a starting terminus. 57: 57: Identified residue ARG81 as a ending terminus. 57: Start terminus ASN-24: NH3+ 57: End terminus ARG-81: COO- 57: 57: Checking for duplicate atoms.... 57: 57: Generating any missing hydrogen atoms and/or adding termini. 57: 57: Now there are 58 residues with 639 atoms 57: 57: Making bonds... 57: 57: Number of bonds was 659, now 654 57: 57: Generating angles, dihedrals and pairs... 57: 57: Making cmap torsions... 57: 57: There are 321 dihedrals, 354 impropers, 963 angles 57: 972 pairs, 654 bonds and 141 virtual sites 57: 57: Total mass 6908.582 a.m.u. 57: 57: Total charge -6.000 e 57: 57: Writing topology 57: 57: Writing coordinate file... 57: 57: --------- PLEASE NOTE ------------ 57: 57: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 57: 57: The Gromos53a6 force field and the spce water model are used. 57: 57: --------- ETON ESAELP ------------ 57: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 57: [----------] 20 tests from G53a6/Pdb2gmxTest (516 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 40 tests from 2 test suites ran. (988 ms total) 57: [ PASSED ] 40 tests. 57/96 Test #57: Pdb2gmx2Test ................................. Passed 1.07 sec test 58 Start 58: Pdb2gmx3Test 58: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/gmxpreprocess/tests 58: Test timeout computed to be: 1920 58: [==========] Running 39 tests from 6 test suites. 58: [----------] Global test environment set-up. 58: [----------] 10 tests from Amber/Pdb2gmxTest 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Before cleaning: 653 pairs 58: Before cleaning: 691 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 128 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (128 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 252 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 255, now 254 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 691 dihedrals, 51 impropers, 457 angles 58: 650 pairs, 254 bonds and 0 virtual sites 58: 58: Total mass 1846.132 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 30 donors and 22 acceptors were found. 58: There are 36 hydrogen bonds 58: Will use HISE for residue 29 58: Will use HISE for residue 32 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS27 HIS29 58: SG90 NE2111 58: HIS29 NE2111 0.987 58: HIS32 NE2135 1.590 1.155 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Before cleaning: 748 pairs 58: Before cleaning: 788 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 149 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (149 atoms, 16 residues) 58: 58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue PHE33 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 281 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 291, now 290 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 788 dihedrals, 72 impropers, 516 angles 58: 736 pairs, 290 bonds and 0 virtual sites 58: 58: Total mass 2088.366 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 22 acceptors were found. 58: There are 26 hydrogen bonds 58: Will use HISE for residue 45 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS45 58: NE295 58: MET46 SD102 1.078 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Before cleaning: 676 pairs 58: Before cleaning: 727 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 132 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (132 atoms, 16 residues) 58: 58: Identified residue ALA34 as a starting terminus. 58: 58: Identified residue ALA49 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 255 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 262, now 261 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 727 dihedrals, 56 impropers, 472 angles 58: 667 pairs, 261 bonds and 0 virtual sites 58: 58: Total mass 1861.124 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 21 acceptors were found. 58: There are 30 hydrogen bonds 58: Will use HISE for residue 60 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS60 58: NE285 58: CYS62 SG98 0.803 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Before cleaning: 603 pairs 58: Before cleaning: 634 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 117 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (117 atoms, 16 residues) 58: 58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue LYS50 as a starting terminus. 58: 58: Identified residue PRO65 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 228 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 233, now 232 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 634 dihedrals, 48 impropers, 419 angles 58: 597 pairs, 232 bonds and 0 virtual sites 58: 58: Total mass 1662.888 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 89 donors and 98 acceptors were found. 58: There are 129 hydrogen bonds 58: Will use HISE for residue 31 58: Will use HISE for residue 51 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS25 HIS31 HIS51 58: SG14 NE264 NE2226 58: HIS31 NE264 1.921 58: HIS51 NE2226 1.498 2.650 58: CYS80 SG477 0.207 1.984 1.570 58: Linking CYS-25 SG-14 and CYS-80 SG-477... 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Before cleaning: 2499 pairs 58: Before cleaning: 2631 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 58 488 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 'A' (488 atoms, 58 residues) 58: 58: Identified residue ASN24 as a starting terminus. 58: 58: Identified residue ARG81 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 58 residues with 936 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 952, now 951 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 2631 dihedrals, 208 impropers, 1704 angles 58: 2469 pairs, 951 bonds and 0 virtual sites 58: 58: Total mass 6908.576 a.m.u. 58: 58: Total charge -6.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Marked 124 virtual sites 58: Added 16 dummy masses 58: Added 26 new constraints 58: Before cleaning: 653 pairs 58: Before cleaning: 691 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 128 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (128 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 252 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 255, now 254 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 691 dihedrals, 51 impropers, 457 angles 58: 650 pairs, 254 bonds and 130 virtual sites 58: 58: Total mass 1846.132 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 30 donors and 22 acceptors were found. 58: There are 36 hydrogen bonds 58: Will use HISE for residue 29 58: Will use HISE for residue 32 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS27 HIS29 58: SG90 NE2111 58: HIS29 NE2111 0.987 58: HIS32 NE2135 1.590 1.155 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Marked 132 virtual sites 58: Added 10 dummy masses 58: Added 19 new constraints 58: Before cleaning: 748 pairs 58: Before cleaning: 788 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 149 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (149 atoms, 16 residues) 58: 58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue PHE33 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 281 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 291, now 290 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 788 dihedrals, 72 impropers, 516 angles 58: 736 pairs, 290 bonds and 133 virtual sites 58: 58: Total mass 2088.366 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 22 acceptors were found. 58: There are 26 hydrogen bonds 58: Will use HISE for residue 45 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS45 58: NE295 58: MET46 SD102 1.078 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Marked 123 virtual sites 58: Added 22 dummy masses 58: Added 35 new constraints 58: Before cleaning: 676 pairs 58: Before cleaning: 727 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 132 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (132 atoms, 16 residues) 58: 58: Identified residue ALA34 as a starting terminus. 58: 58: Identified residue ALA49 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 255 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 262, now 261 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 727 dihedrals, 56 impropers, 472 angles 58: 667 pairs, 261 bonds and 132 virtual sites 58: 58: Total mass 1861.124 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 21 acceptors were found. 58: There are 30 hydrogen bonds 58: Will use HISE for residue 60 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS60 58: NE285 58: CYS62 SG98 0.803 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Marked 111 virtual sites 58: Added 18 dummy masses 58: Added 31 new constraints 58: Before cleaning: 603 pairs 58: Before cleaning: 634 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 117 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (117 atoms, 16 residues) 58: 58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue LYS50 as a starting terminus. 58: 58: Identified residue PRO65 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 228 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 233, now 232 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 634 dihedrals, 48 impropers, 419 angles 58: 597 pairs, 232 bonds and 116 virtual sites 58: 58: Total mass 1662.888 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 58: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 89 donors and 98 acceptors were found. 58: There are 129 hydrogen bonds 58: Will use HISE for residue 31 58: Will use HISE for residue 51 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS25 HIS31 HIS51 58: SG14 NE264 NE2226 58: HIS31 NE264 1.921 58: HIS51 NE2226 1.498 2.650 58: CYS80 SG477 0.207 1.984 1.570 58: Linking CYS-25 SG-14 and CYS-80 SG-477... 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Marked 447 virtual sites 58: Added 58 dummy masses 58: Added 101 new constraints 58: Before cleaning: 2499 pairs 58: Before cleaning: 2631 dihedrals 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 58 488 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 'A' (488 atoms, 58 residues) 58: 58: Identified residue ASN24 as a starting terminus. 58: 58: Identified residue ARG81 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 58 residues with 936 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 952, now 951 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 2631 dihedrals, 208 impropers, 1704 angles 58: 2469 pairs, 951 bonds and 462 virtual sites 58: 58: Total mass 6908.576 a.m.u. 58: 58: Total charge -6.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 58: 58: The Amber99sb-ildn force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (61 ms) 58: [----------] 10 tests from Amber/Pdb2gmxTest (310 ms total) 58: 58: [----------] 1 test from AmberTip4p/Pdb2gmxTest 58: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/amber99sb-ildn.ff/rna.arn 58: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 58: 58: going to rename amber99sb-ildn.ff/aminoacids.r2b 58: 58: going to rename amber99sb-ildn.ff/dna.r2b 58: 58: going to rename amber99sb-ildn.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 58: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 2 4 (only water) 58: 58: All occupancies are one 58: 58: Reading residue database... (Amber99sb-ildn) 58: 58: Processing chain 1 (4 atoms, 2 residues) 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 2 residues with 8 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 4, now 4 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 2 angles 58: 0 pairs, 4 bonds and 0 virtual sites 58: 58: Total mass 36.032 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 58: 58: The Amber99sb-ildn force field and the tip4p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (10 ms) 58: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 ms total) 58: 58: [----------] 12 tests from Charmm/Pdb2gmxTest 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 653 pairs 58: Before cleaning: 663 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 128 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (128 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 252 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 254, now 254 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 663 dihedrals, 48 impropers, 457 angles 58: 650 pairs, 254 bonds and 0 virtual sites 58: 58: Total mass 1846.115 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (20 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 30 donors and 22 acceptors were found. 58: There are 36 hydrogen bonds 58: Will use HISE for residue 29 58: Will use HISE for residue 32 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS27 HIS29 58: SG90 NE2111 58: HIS29 NE2111 0.987 58: HIS32 NE2135 1.590 1.155 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 748 pairs 58: Before cleaning: 778 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 149 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (149 atoms, 16 residues) 58: 58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue PHE33 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus PHE-33: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 281 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 290, now 290 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 778 dihedrals, 49 impropers, 516 angles 58: 736 pairs, 290 bonds and 0 virtual sites 58: 58: Total mass 2088.361 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 22 acceptors were found. 58: There are 26 hydrogen bonds 58: Will use HISE for residue 45 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS45 58: NE295 58: MET46 SD102 1.078 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 676 pairs 58: Before cleaning: 696 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 132 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (132 atoms, 16 residues) 58: 58: Identified residue ALA34 as a starting terminus. 58: 58: Identified residue ALA49 as a ending terminus. 58: Start terminus ALA-34: NH3+ 58: End terminus ALA-49: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 255 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 261, now 261 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 696 dihedrals, 39 impropers, 472 angles 58: 667 pairs, 261 bonds and 0 virtual sites 58: 58: Total mass 1861.130 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (20 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 21 acceptors were found. 58: There are 30 hydrogen bonds 58: Will use HISE for residue 60 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS60 58: NE285 58: CYS62 SG98 0.803 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 603 pairs 58: Before cleaning: 618 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 117 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (117 atoms, 16 residues) 58: 58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue LYS50 as a starting terminus. 58: 58: Identified residue PRO65 as a ending terminus. 58: Start terminus LYS-50: NH3+ 58: End terminus PRO-65: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 228 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 232, now 232 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 618 dihedrals, 38 impropers, 419 angles 58: 597 pairs, 232 bonds and 0 virtual sites 58: 58: Total mass 1662.885 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (19 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 89 donors and 98 acceptors were found. 58: There are 129 hydrogen bonds 58: Will use HISE for residue 31 58: Will use HISE for residue 51 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS25 HIS31 HIS51 58: SG14 NE264 NE2226 58: HIS31 NE264 1.921 58: HIS51 NE2226 1.498 2.650 58: CYS80 SG477 0.207 1.984 1.570 58: Linking CYS-25 SG-14 and CYS-80 SG-477... 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 2499 pairs 58: Before cleaning: 2524 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 58 488 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (488 atoms, 58 residues) 58: 58: Identified residue ASN24 as a starting terminus. 58: 58: Identified residue ARG81 as a ending terminus. 58: Start terminus ASN-24: NH3+ 58: End terminus ARG-81: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 58 residues with 936 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 951, now 951 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 56 cmap torsion pairs 58: 58: There are 2524 dihedrals, 149 impropers, 1704 angles 58: 2469 pairs, 951 bonds and 0 virtual sites 58: 58: Total mass 6908.566 a.m.u. 58: 58: Total charge -6.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (50 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 39 pairs 58: Before cleaning: 39 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 58: Read 'GLU', 9 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 58: 58: chain #res #atoms 58: 58: 1 'X' 1 9 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'X' (9 atoms, 1 residues) 58: 58: Identified residue GLU1 as a starting terminus. 58: 58: Identified residue GLU1 as a ending terminus. 58: Start terminus GLU-1: NH3+ 58: End terminus GLU-1: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 1 residues with 18 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 17, now 17 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 39 dihedrals, 2 impropers, 30 angles 58: 39 pairs, 17 bonds and 0 virtual sites 58: 58: Total mass 146.123 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 124 virtual sites 58: Added 16 dummy masses 58: Added 26 new constraints 58: Before cleaning: 653 pairs 58: Before cleaning: 663 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 128 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (128 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 252 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 254, now 254 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 663 dihedrals, 48 impropers, 457 angles 58: 650 pairs, 254 bonds and 130 virtual sites 58: 58: Total mass 1846.115 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/A.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 30 donors and 22 acceptors were found. 58: There are 36 hydrogen bonds 58: Will use HISE for residue 29 58: Will use HISE for residue 32 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS27 HIS29 58: SG90 NE2111 58: HIS29 NE2111 0.987 58: HIS32 NE2135 1.590 1.155 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 132 virtual sites 58: Added 10 dummy masses 58: Added 19 new constraints 58: Before cleaning: 748 pairs 58: Before cleaning: 778 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb... 58: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 149 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (149 atoms, 16 residues) 58: 58: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue PHE33 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus PHE-33: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 281 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 290, now 290 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 778 dihedrals, 49 impropers, 516 angles 58: 736 pairs, 290 bonds and 133 virtual sites 58: 58: Total mass 2088.361 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/B.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 22 acceptors were found. 58: There are 26 hydrogen bonds 58: Will use HISE for residue 45 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS45 58: NE295 58: MET46 SD102 1.078 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 123 virtual sites 58: Added 22 dummy masses 58: Added 35 new constraints 58: Before cleaning: 676 pairs 58: Before cleaning: 696 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb... 58: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 132 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (132 atoms, 16 residues) 58: 58: Identified residue ALA34 as a starting terminus. 58: 58: Identified residue ALA49 as a ending terminus. 58: Start terminus ALA-34: NH3+ 58: End terminus ALA-49: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 255 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 261, now 261 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 696 dihedrals, 39 impropers, 472 angles 58: 667 pairs, 261 bonds and 132 virtual sites 58: 58: Total mass 1861.130 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/C.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 22 donors and 21 acceptors were found. 58: There are 30 hydrogen bonds 58: Will use HISE for residue 60 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS60 58: NE285 58: CYS62 SG98 0.803 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 111 virtual sites 58: Added 18 dummy masses 58: Added 31 new constraints 58: Before cleaning: 603 pairs 58: Before cleaning: 618 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb... 58: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 58: 58: chain #res #atoms 58: 58: 1 ' ' 16 117 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 (117 atoms, 16 residues) 58: 58: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 58: 58: Identified residue LYS50 as a starting terminus. 58: 58: Identified residue PRO65 as a ending terminus. 58: Start terminus LYS-50: NH3+ 58: End terminus PRO-65: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 228 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 232, now 232 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 14 cmap torsion pairs 58: 58: There are 618 dihedrals, 38 impropers, 419 angles 58: 597 pairs, 232 bonds and 116 virtual sites 58: 58: Total mass 1662.885 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/D.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 89 donors and 98 acceptors were found. 58: There are 129 hydrogen bonds 58: Will use HISE for residue 31 58: Will use HISE for residue 51 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS25 HIS31 HIS51 58: SG14 NE264 NE2226 58: HIS31 NE264 1.921 58: HIS51 NE2226 1.498 2.650 58: CYS80 SG477 0.207 1.984 1.570 58: Linking CYS-25 SG-14 and CYS-80 SG-477... 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 447 virtual sites 58: Added 58 dummy masses 58: Added 101 new constraints 58: Before cleaning: 2499 pairs 58: Before cleaning: 2524 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb... 58: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 58 488 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (488 atoms, 58 residues) 58: 58: Identified residue ASN24 as a starting terminus. 58: 58: Identified residue ARG81 as a ending terminus. 58: Start terminus ASN-24: NH3+ 58: End terminus ARG-81: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 58 residues with 936 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 951, now 951 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 56 cmap torsion pairs 58: 58: There are 2524 dihedrals, 149 impropers, 1704 angles 58: 2469 pairs, 951 bonds and 462 virtual sites 58: 58: Total mass 6908.566 a.m.u. 58: 58: Total charge -6.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/E.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (55 ms) 58: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Marked 8 virtual sites 58: Added 2 dummy masses 58: Added 3 new constraints 58: Before cleaning: 39 pairs 58: Before cleaning: 39 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb... 58: Read 'GLU', 9 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 58: 58: chain #res #atoms 58: 58: 1 'X' 1 9 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'X' (9 atoms, 1 residues) 58: 58: Identified residue GLU1 as a starting terminus. 58: 58: Identified residue GLU1 as a ending terminus. 58: Start terminus GLU-1: NH3+ 58: End terminus GLU-1: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 1 residues with 18 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 17, now 17 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 39 dihedrals, 2 impropers, 30 angles 58: 39 pairs, 17 bonds and 9 virtual sites 58: 58: Total mass 146.123 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/monomer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (10 ms) 58: [----------] 12 tests from Charmm/Pdb2gmxTest (299 ms total) 58: 58: [----------] 8 tests from ChainSep/Pdb2gmxTest 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 651 pairs 58: Before cleaning: 661 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on changing chain id only (ignoring TER records). 58: 58: Merged chains into joint molecule definitions at 2 places. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 16 127 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (127 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue GLU5 as a ending terminus. 58: 58: Identified residue PHE6 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus GLU-5: COO- 58: Start terminus PHE-6: NH3+ 58: End terminus MET-12: COO- 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 258 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 258, now 258 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 10 cmap torsion pairs 58: 58: There are 661 dihedrals, 46 impropers, 463 angles 58: 648 pairs, 258 bonds and 0 virtual sites 58: 58: Total mass 1882.146 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (21 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 123 pairs 58: Before cleaning: 123 dihedrals 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 10 donors and 7 acceptors were found. 58: There are 7 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: HIS8 58: NE223 58: MET12 SD55 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 317 pairs 58: Before cleaning: 322 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 211 pairs 58: Before cleaning: 216 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on changing chain id only (ignoring TER records). 58: 58: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 4 28 58: 58: 2 'B' 7 58 58: 58: 3 'C' 5 41 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (28 atoms, 4 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue GLU5 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus GLU-5: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 4 residues with 51 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 50, now 50 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 2 cmap torsion pairs 58: 58: There are 123 dihedrals, 9 impropers, 88 angles 58: 123 pairs, 50 bonds and 0 virtual sites 58: 58: Total mass 434.421 a.m.u. 58: 58: Total charge -2.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (58 atoms, 7 residues) 58: 58: Identified residue PHE6 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: Start terminus PHE-6: NH3+ 58: End terminus MET-12: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 7 residues with 124 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 125, now 125 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 5 cmap torsion pairs 58: 58: There are 322 dihedrals, 19 impropers, 227 angles 58: 314 pairs, 125 bonds and 0 virtual sites 58: 58: Total mass 846.083 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Processing chain 3 'C' (41 atoms, 5 residues) 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 5 residues with 83 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 83, now 83 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 3 cmap torsion pairs 58: 58: There are 216 dihedrals, 18 impropers, 148 angles 58: 211 pairs, 83 bonds and 0 virtual sites 58: 58: Total mass 601.643 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 51 atoms 4 residues 58: 58: Including chain 2 in system: 124 atoms 7 residues 58: 58: Including chain 3 in system: 83 atoms 5 residues 58: 58: Now there are 258 atoms and 16 residues 58: 58: Total mass in system 1882.146 a.m.u. 58: 58: Total charge in system 0.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (18 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 651 pairs 58: Before cleaning: 661 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records only (ignoring chain id). 58: 58: Merged chains into joint molecule definitions at 2 places. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 16 127 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (127 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ILE9 as a ending terminus. 58: 58: Identified residue LYS10 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ILE-9: COO- 58: Start terminus LYS-10: NH3+ 58: End terminus MET-12: COO- 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 258 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 258, now 258 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 10 cmap torsion pairs 58: 58: There are 661 dihedrals, 46 impropers, 463 angles 58: 648 pairs, 258 bonds and 0 virtual sites 58: 58: Total mass 1882.146 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 10 donors and 12 acceptors were found. 58: There are 13 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 58: SG9 58: HIS8 NE251 1.055 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 288 pairs 58: Before cleaning: 293 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 152 pairs 58: Before cleaning: 152 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 211 pairs 58: Before cleaning: 216 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records only (ignoring chain id). 58: 58: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 8 61 58: 58: 2 'B' 3 25 58: 58: 3 'C' 5 41 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (61 atoms, 8 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ILE9 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ILE-9: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 8 residues with 114 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 115, now 115 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 6 cmap torsion pairs 58: 58: There are 293 dihedrals, 23 impropers, 203 angles 58: 285 pairs, 115 bonds and 0 virtual sites 58: 58: Total mass 888.952 a.m.u. 58: 58: Total charge -2.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (25 atoms, 3 residues) 58: 58: Identified residue LYS10 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: Start terminus LYS-10: NH3+ 58: End terminus MET-12: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 61 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 60, now 60 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 152 dihedrals, 5 impropers, 112 angles 58: 152 pairs, 60 bonds and 0 virtual sites 58: 58: Total mass 391.552 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Processing chain 3 'C' (41 atoms, 5 residues) 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 5 residues with 83 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 83, now 83 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 3 cmap torsion pairs 58: 58: There are 216 dihedrals, 18 impropers, 148 angles 58: 211 pairs, 83 bonds and 0 virtual sites 58: 58: Total mass 601.643 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 114 atoms 8 residues 58: 58: Including chain 2 in system: 61 atoms 3 residues 58: 58: Including chain 3 in system: 83 atoms 5 residues 58: 58: Now there are 258 atoms and 16 residues 58: 58: Total mass in system 1882.146 a.m.u. 58: 58: Total charge in system 0.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 650 pairs 58: Before cleaning: 660 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: Merged chains into joint molecule definitions at 3 places. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 16 127 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (127 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue GLU5 as a ending terminus. 58: 58: Identified residue PHE6 as a starting terminus. 58: 58: Identified residue ILE9 as a ending terminus. 58: 58: Identified residue LYS10 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus GLU-5: COO- 58: Start terminus PHE-6: NH3+ 58: End terminus ILE-9: COO- 58: Start terminus LYS-10: NH3+ 58: End terminus MET-12: COO- 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 261 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 260, now 260 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 8 cmap torsion pairs 58: 58: There are 660 dihedrals, 45 impropers, 466 angles 58: 647 pairs, 260 bonds and 0 virtual sites 58: 58: Total mass 1900.162 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 58: 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 123 pairs 58: Before cleaning: 123 dihedrals 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 6 donors and 4 acceptors were found. 58: There are 3 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 164 pairs 58: Before cleaning: 169 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 152 pairs 58: Before cleaning: 152 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 211 pairs 58: Before cleaning: 216 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 58: 58: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 4 28 58: 58: 2 'B' 4 33 58: 58: 3 'B' 3 25 58: 58: 4 'C' 5 41 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (28 atoms, 4 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue GLU5 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus GLU-5: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 4 residues with 51 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 50, now 50 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 2 cmap torsion pairs 58: 58: There are 123 dihedrals, 9 impropers, 88 angles 58: 123 pairs, 50 bonds and 0 virtual sites 58: 58: Total mass 434.421 a.m.u. 58: 58: Total charge -2.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (33 atoms, 4 residues) 58: 58: Identified residue PHE6 as a starting terminus. 58: 58: Identified residue ILE9 as a ending terminus. 58: Start terminus PHE-6: NH3+ 58: End terminus ILE-9: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 4 residues with 66 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 67, now 67 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 2 cmap torsion pairs 58: 58: There are 169 dihedrals, 13 impropers, 118 angles 58: 161 pairs, 67 bonds and 0 virtual sites 58: 58: Total mass 472.547 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Processing chain 3 'B' (25 atoms, 3 residues) 58: 58: Identified residue LYS10 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: Start terminus LYS-10: NH3+ 58: End terminus MET-12: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 61 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 60, now 60 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 152 dihedrals, 5 impropers, 112 angles 58: 152 pairs, 60 bonds and 0 virtual sites 58: 58: Total mass 391.552 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Processing chain 4 'C' (41 atoms, 5 residues) 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 5 residues with 83 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 83, now 83 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 3 cmap torsion pairs 58: 58: There are 216 dihedrals, 18 impropers, 148 angles 58: 211 pairs, 83 bonds and 0 virtual sites 58: 58: Total mass 601.643 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 51 atoms 4 residues 58: 58: Including chain 2 in system: 66 atoms 4 residues 58: 58: Including chain 3 in system: 61 atoms 3 residues 58: 58: Including chain 4 in system: 83 atoms 5 residues 58: 58: Now there are 261 atoms and 16 residues 58: 58: Total mass in system 1900.162 a.m.u. 58: 58: Total charge in system 0.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (18 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 25 donors and 23 acceptors were found. 58: There are 41 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 652 pairs 58: Before cleaning: 662 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records and chain id changing. 58: 58: Merged chains into joint molecule definitions at 1 places. 58: 58: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 16 127 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (127 atoms, 16 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus MET-12: COO- 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 255 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 256, now 256 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 12 cmap torsion pairs 58: 58: There are 662 dihedrals, 47 impropers, 460 angles 58: 649 pairs, 256 bonds and 0 virtual sites 58: 58: Total mass 1864.131 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (20 ms) 58: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: Analysing hydrogen-bonding network for automated assignment of histidine 58: protonation. 14 donors and 15 acceptors were found. 58: There are 20 hydrogen bonds 58: Will use HISE for residue 8 58: 9 out of 9 lines of specbond.dat converted successfully 58: Special Atom Distance matrix: 58: CYS3 HIS8 58: SG9 NE251 58: HIS8 NE251 1.055 58: MET12 SD83 0.763 0.990 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 441 pairs 58: Before cleaning: 446 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 211 pairs 58: Before cleaning: 216 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 58: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records and chain id changing. 58: 58: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 11 86 58: 58: 2 'C' 5 41 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (86 atoms, 11 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue MET12 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus MET-12: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 11 residues with 172 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 173, now 173 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 9 cmap torsion pairs 58: 58: There are 446 dihedrals, 29 impropers, 312 angles 58: 438 pairs, 173 bonds and 0 virtual sites 58: 58: Total mass 1262.488 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'C' (41 atoms, 5 residues) 58: 58: Identified residue ASN13 as a starting terminus. 58: 58: Identified residue SER17 as a ending terminus. 58: Start terminus ASN-13: NH3+ 58: End terminus SER-17: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 5 residues with 83 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 83, now 83 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 3 cmap torsion pairs 58: 58: There are 216 dihedrals, 18 impropers, 148 angles 58: 211 pairs, 83 bonds and 0 virtual sites 58: 58: Total mass 601.643 a.m.u. 58: 58: Total charge 1.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 172 atoms 11 residues 58: 58: Including chain 2 in system: 83 atoms 5 residues 58: 58: Now there are 255 atoms and 16 residues 58: 58: Total mass in system 1864.131 a.m.u. 58: 58: Total charge in system 0.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (16 ms) 58: [----------] 8 tests from ChainSep/Pdb2gmxTest (156 ms total) 58: 58: [----------] 4 tests from ChainChanges/Pdb2gmxTest 58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 83 pairs 58: Before cleaning: 83 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 145 pairs 58: Before cleaning: 150 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 58: Read 'Fragments of peptides and ions', 47 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on changing chain id only (ignoring TER records). 58: 58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 3 19 58: 58: 2 'B' 3 28 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (19 atoms, 3 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ASP4 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ASP-4: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 36 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 35, now 35 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 83 dihedrals, 6 impropers, 61 angles 58: 83 pairs, 35 bonds and 0 virtual sites 58: 58: Total mass 306.314 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (28 atoms, 3 residues) 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue TRP20 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus TRP-20: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 57 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 58, now 58 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 150 dihedrals, 5 impropers, 103 angles 58: 142 pairs, 58 bonds and 0 virtual sites 58: 58: Total mass 404.468 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 36 atoms 3 residues 58: 58: Including chain 2 in system: 57 atoms 3 residues 58: 58: Now there are 93 atoms and 6 residues 58: 58: Total mass in system 710.782 a.m.u. 58: 58: Total charge in system -1.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 83 pairs 58: Before cleaning: 83 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 145 pairs 58: Before cleaning: 150 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 58: Read 'Fragments of peptides and ions', 47 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records only (ignoring chain id). 58: 58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 3 19 58: 58: 2 'B' 3 28 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (19 atoms, 3 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ASP4 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ASP-4: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 36 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 35, now 35 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 83 dihedrals, 6 impropers, 61 angles 58: 83 pairs, 35 bonds and 0 virtual sites 58: 58: Total mass 306.314 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (28 atoms, 3 residues) 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue TRP20 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus TRP-20: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 57 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 58, now 58 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 150 dihedrals, 5 impropers, 103 angles 58: 142 pairs, 58 bonds and 0 virtual sites 58: 58: Total mass 404.468 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 36 atoms 3 residues 58: 58: Including chain 2 in system: 57 atoms 3 residues 58: 58: Now there are 93 atoms and 6 residues 58: 58: Total mass in system 710.782 a.m.u. 58: 58: Total charge in system -1.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 83 pairs 58: Before cleaning: 83 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 145 pairs 58: Before cleaning: 150 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 58: Read 'Fragments of peptides and ions', 47 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 3 19 58: 58: 2 'B' 3 28 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (19 atoms, 3 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ASP4 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ASP-4: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 36 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 35, now 35 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 83 dihedrals, 6 impropers, 61 angles 58: 83 pairs, 35 bonds and 0 virtual sites 58: 58: Total mass 306.314 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (28 atoms, 3 residues) 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue TRP20 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus TRP-20: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 57 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 58, now 58 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 150 dihedrals, 5 impropers, 103 angles 58: 142 pairs, 58 bonds and 0 virtual sites 58: 58: Total mass 404.468 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 36 atoms 3 residues 58: 58: Including chain 2 in system: 57 atoms 3 residues 58: 58: Now there are 93 atoms and 6 residues 58: 58: Total mass in system 710.782 a.m.u. 58: 58: Total charge in system -1.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 58: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 83 pairs 58: Before cleaning: 83 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 145 pairs 58: Before cleaning: 150 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb... 58: Read 'Fragments of peptides and ions', 47 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records and chain id changing. 58: 58: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 3 19 58: 58: 2 'B' 3 28 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (19 atoms, 3 residues) 58: 58: Identified residue ALA2 as a starting terminus. 58: 58: Identified residue ASP4 as a ending terminus. 58: Start terminus ALA-2: NH3+ 58: End terminus ASP-4: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 36 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 35, now 35 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 83 dihedrals, 6 impropers, 61 angles 58: 83 pairs, 35 bonds and 0 virtual sites 58: 58: Total mass 306.314 a.m.u. 58: 58: Total charge -1.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'B' (28 atoms, 3 residues) 58: 58: Identified residue THR18 as a starting terminus. 58: 58: Identified residue TRP20 as a ending terminus. 58: Start terminus THR-18: NH3+ 58: End terminus TRP-20: COO- 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 3 residues with 57 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 58, now 58 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 1 cmap torsion pairs 58: 58: There are 150 dihedrals, 5 impropers, 103 angles 58: 142 pairs, 58 bonds and 0 virtual sites 58: 58: Total mass 404.468 a.m.u. 58: 58: Total charge -0.000 e 58: 58: Writing topology 58: 58: Including chain 1 in system: 36 atoms 3 residues 58: 58: Including chain 2 in system: 57 atoms 3 residues 58: 58: Now there are 93 atoms and 6 residues 58: 58: Total mass in system 710.782 a.m.u. 58: 58: Total charge in system -1.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/fragments.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (12 ms) 58: [----------] 4 tests from ChainChanges/Pdb2gmxTest (50 ms total) 58: 58: [----------] 4 tests from Cyclic/Pdb2gmxTest 58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: WARNING: all CONECT records are ignored 58: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 58: 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 6040 pairs 58: Before cleaning: 6605 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 6040 pairs 58: Before cleaning: 6605 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 58: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 58: 58: Moved all the water blocks to the end 58: 58: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 58: 58: chain #res #atoms 58: 58: 1 'P' 71 1527 58: 58: 2 'Q' 71 1527 58: 58: 3 'Q' 7 7 58: 58: 4 ' ' 10 10 (only water) 58: 58: 5 ' ' 16 16 (only water) 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'P' (1527 atoms, 71 residues) 58: 58: Identified residue G1 as a starting terminus. 58: 58: Identified residue U71 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 71 residues with 2297 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 2481, now 2481 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 6605 dihedrals, 183 impropers, 4434 angles 58: 5827 pairs, 2481 bonds and 0 virtual sites 58: 58: Total mass 22984.514 a.m.u. 58: 58: Total charge -71.000 e 58: 58: Writing topology 58: 58: Processing chain 2 'Q' (1527 atoms, 71 residues) 58: 58: Identified residue G1 as a starting terminus. 58: 58: Identified residue U71 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 71 residues with 2297 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: Number of bonds was 2481, now 2481 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 6605 dihedrals, 183 impropers, 4434 angles 58: 5827 pairs, 2481 bonds and 0 virtual sites 58: 58: Total mass 22984.514 a.m.u. 58: 58: Total charge -71.000 e 58: 58: Writing topology 58: 58: Processing chain 3 'Q' (7 atoms, 7 residues) 58: 58: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 58: 58: Disabling further notes about ions. 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 7 residues with 7 atoms 58: Chain time... 58: 58: Making bonds... 58: 58: No bonds 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 0 angles 58: 0 pairs, 0 bonds and 0 virtual sites 58: 58: Total mass 170.135 a.m.u. 58: 58: Total charge 14.000 e 58: 58: Writing topology 58: 58: Processing chain 4 (10 atoms, 10 residues) 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 10 residues with 30 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 30, now 30 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 30 angles 58: 0 pairs, 30 bonds and 0 virtual sites 58: 58: Total mass 180.154 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Processing chain 5 (16 atoms, 16 residues) 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 48 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 48, now 48 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 48 angles 58: 0 pairs, 48 bonds and 0 virtual sites 58: 58: Total mass 288.246 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Including chain 1 in system: 2297 atoms 71 residues 58: 58: Including chain 2 in system: 2297 atoms 71 residues 58: 58: Including chain 3 in system: 7 atoms 7 residues 58: 58: Including chain 4 in system: 30 atoms 10 residues 58: 58: Including chain 5 in system: 48 atoms 16 residues 58: 58: Now there are 4679 atoms and 175 residues 58: 58: Total mass in system 46607.562 a.m.u. 58: 58: Total charge in system -128.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (171 ms) 58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 2325 pairs 58: Before cleaning: 2325 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 58: Read 'CARNOCYCLIN-A', 413 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 60 413 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (413 atoms, 60 residues) 58: 58: Identified residue LEU1 as a starting terminus. 58: 58: Identified residue LEU60 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 60 residues with 878 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 880, now 880 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 60 cmap torsion pairs 58: 58: There are 2325 dihedrals, 137 impropers, 1614 angles 58: 2319 pairs, 880 bonds and 0 virtual sites 58: 58: Total mass 5866.087 a.m.u. 58: 58: Total charge 4.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (47 ms) 58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: WARNING: all CONECT records are ignored 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 12080 pairs 58: Before cleaning: 13210 dihedrals 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 58: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: Moved all the water blocks to the end 58: 58: Merged chains into joint molecule definitions at 2 places. 58: 58: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 58: 58: chain #res #atoms 58: 58: 1 'P' 149 3061 58: 58: 2 ' ' 10 10 (only water) 58: 58: 3 ' ' 16 16 (only water) 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'P' (3061 atoms, 149 residues) 58: 58: Identified residue G1 as a starting terminus. 58: 58: Identified residue U71 as a ending terminus. 58: 58: Identified residue G1 as a starting terminus. 58: 58: Identified residue U71 as a ending terminus. 58: 58: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 58: 58: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 58: 58: Disabling further notes about ions. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 149 residues with 4601 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 4962, now 4962 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 13210 dihedrals, 366 impropers, 8868 angles 58: 11654 pairs, 4962 bonds and 0 virtual sites 58: 58: Total mass 46139.162 a.m.u. 58: 58: Total charge -128.000 e 58: 58: Writing topology 58: 58: Processing chain 2 (10 atoms, 10 residues) 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 10 residues with 30 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 30, now 30 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 30 angles 58: 0 pairs, 30 bonds and 0 virtual sites 58: 58: Total mass 180.154 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Processing chain 3 (16 atoms, 16 residues) 58: 58: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 16 residues with 48 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 48, now 48 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 0 dihedrals, 0 impropers, 48 angles 58: 0 pairs, 48 bonds and 0 virtual sites 58: 58: Total mass 288.246 a.m.u. 58: 58: Total charge 0.000 e 58: 58: Including chain 1 in system: 4601 atoms 149 residues 58: 58: Including chain 2 in system: 30 atoms 10 residues 58: 58: Including chain 3 in system: 48 atoms 16 residues 58: 58: Now there are 4679 atoms and 175 residues 58: 58: Total mass in system 46607.562 a.m.u. 58: 58: Total charge in system -128.000 e 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (270 ms) 58: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.r2b 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.r2b 58: All occupancies are one 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/atomtypes.atp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.rtp 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/lipids.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.hdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.n.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.c.tdb 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.c.tdb 58: 9 out of 9 lines of specbond.dat converted successfully 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/aminoacids.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/dna.arn 58: Opening force field file /build/reproducible-path/gromacs-2025.1/share/top/charmm27.ff/rna.arn 58: Before cleaning: 2325 pairs 58: Before cleaning: 2325 dihedrals 58: Using the Charmm27 force field in directory charmm27.ff 58: 58: going to rename charmm27.ff/aminoacids.r2b 58: 58: going to rename charmm27.ff/rna.r2b 58: Reading /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 58: Read 'CARNOCYCLIN-A', 413 atoms 58: 58: Analyzing pdb file 58: Splitting chemical chains based on TER records or chain id changing. 58: 58: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 58: 58: chain #res #atoms 58: 58: 1 'A' 60 413 58: 58: All occupancies are one 58: 58: Reading residue database... (Charmm27) 58: 58: Processing chain 1 'A' (413 atoms, 60 residues) 58: 58: Identified residue LEU1 as a starting terminus. 58: 58: Identified residue LEU60 as a ending terminus. 58: 58: Checking for duplicate atoms.... 58: 58: Generating any missing hydrogen atoms and/or adding termini. 58: 58: Now there are 60 residues with 878 atoms 58: 58: Making bonds... 58: 58: Number of bonds was 880, now 880 58: 58: Generating angles, dihedrals and pairs... 58: 58: Making cmap torsions... 58: 58: There are 60 cmap torsion pairs 58: 58: There are 2325 dihedrals, 137 impropers, 1614 angles 58: 2319 pairs, 880 bonds and 0 virtual sites 58: 58: Total mass 5866.087 a.m.u. 58: 58: Total charge 4.000 e 58: 58: Writing topology 58: 58: Writing coordinate file... 58: 58: --------- PLEASE NOTE ------------ 58: 58: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 58: 58: The Charmm27 force field and the tip3p water model are used. 58: 58: --------- ETON ESAELP ------------ 58: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (46 ms) 58: [----------] 4 tests from Cyclic/Pdb2gmxTest (536 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 39 tests from 6 test suites ran. (1363 ms total) 58: [ PASSED ] 39 tests. 58/96 Test #58: Pdb2gmx3Test ................................. Passed 1.44 sec test 59 Start 59: CorrelationsTest 59: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/CorrelationsTest.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/correlationfunctions/tests 59: Test timeout computed to be: 30 59: [==========] Running 21 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 10 tests from AutocorrTest 59: [ RUN ] AutocorrTest.EacNormal 59: [ OK ] AutocorrTest.EacNormal (26 ms) 59: [ RUN ] AutocorrTest.EacNoNormalize 59: [ OK ] AutocorrTest.EacNoNormalize (19 ms) 59: [ RUN ] AutocorrTest.EacCos 59: [ OK ] AutocorrTest.EacCos (25 ms) 59: [ RUN ] AutocorrTest.EacVector 59: [ OK ] AutocorrTest.EacVector (46 ms) 59: [ RUN ] AutocorrTest.EacRcross 59: [ OK ] AutocorrTest.EacRcross (0 ms) 59: [ RUN ] AutocorrTest.EacP0 59: [ OK ] AutocorrTest.EacP0 (49 ms) 59: [ RUN ] AutocorrTest.EacP1 59: [ OK ] AutocorrTest.EacP1 (62 ms) 59: [ RUN ] AutocorrTest.EacP2 59: [ OK ] AutocorrTest.EacP2 (104 ms) 59: [ RUN ] AutocorrTest.EacP3 59: [ OK ] AutocorrTest.EacP3 (1 ms) 59: [ RUN ] AutocorrTest.EacP4 59: [ OK ] AutocorrTest.EacP4 (38 ms) 59: [----------] 10 tests from AutocorrTest (375 ms total) 59: 59: [----------] 10 tests from ExpfitTest 59: [ RUN ] ExpfitTest.EffnEXP1 59: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 59: [ RUN ] ExpfitTest.EffnEXP2 59: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 59: [ RUN ] ExpfitTest.EffnEXPEXP 59: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 59: [ RUN ] ExpfitTest.EffnEXP5 59: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 59: [ RUN ] ExpfitTest.EffnEXP7 59: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 59: [ RUN ] ExpfitTest.EffnEXP9 59: [ OK ] ExpfitTest.EffnEXP9 (6 ms) 59: [ RUN ] ExpfitTest.EffnERF 59: [ OK ] ExpfitTest.EffnERF (9 ms) 59: [ RUN ] ExpfitTest.EffnERREST 59: [ OK ] ExpfitTest.EffnERREST (1 ms) 59: [ RUN ] ExpfitTest.EffnVAC 59: [ OK ] ExpfitTest.EffnVAC (3 ms) 59: [ RUN ] ExpfitTest.EffnPRES 59: [ OK ] ExpfitTest.EffnPRES (6 ms) 59: [----------] 10 tests from ExpfitTest (31 ms total) 59: 59: [----------] 1 test from ManyAutocorrelationTest 59: [ RUN ] ManyAutocorrelationTest.Empty 59: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 59: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 21 tests from 3 test suites ran. (410 ms total) 59: [ PASSED ] 21 tests. 59/96 Test #59: CorrelationsTest ............................. Passed 0.49 sec test 60 Start 60: AnalysisDataUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/analysisdata/tests 60: Test timeout computed to be: 30 60: [==========] Running 69 tests from 14 test suites. 60: [----------] Global test environment set-up. 60: [----------] 3 tests from AnalysisDataInitializationTest 60: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 60: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 60: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 60: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 60: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 60: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 60: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 60: 60: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 60: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 60: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 60: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 60: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 60: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 60: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 60: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 60: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 60: 60: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 60: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 60: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 60: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 60: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 60: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 60: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 60: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 60: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 60: 60: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 60: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 60: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 60: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 60: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 60: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 60: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 60: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 60: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 60: 60: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 60: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 60: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 60: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 60: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 60: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 60: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 60: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 60: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 60: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 60: 60: [----------] 4 tests from AnalysisArrayDataTest 60: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 60: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 60: [ RUN ] AnalysisArrayDataTest.StorageWorks 60: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 60: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 60: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 60: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 60: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 60: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 60: 60: [----------] 6 tests from AverageModuleTest 60: [ RUN ] AverageModuleTest.BasicTest 60: [ OK ] AverageModuleTest.BasicTest (0 ms) 60: [ RUN ] AverageModuleTest.HandlesMultipointData 60: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 60: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 60: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 60: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 60: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 60: [ RUN ] AverageModuleTest.CanCustomizeXAxis 60: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 60: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 60: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 60: [----------] 6 tests from AverageModuleTest (1 ms total) 60: 60: [----------] 2 tests from FrameAverageModuleTest 60: [ RUN ] FrameAverageModuleTest.BasicTest 60: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 60: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 60: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 60: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 60: 60: [----------] 7 tests from AnalysisHistogramSettingsTest 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 60: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 60: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 60: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 60: 60: [----------] 2 tests from SimpleHistogramModuleTest 60: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 60: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 60: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 60: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 60: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 60: 60: [----------] 3 tests from WeightedHistogramModuleTest 60: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 60: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 60: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 60: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 60: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 60: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 60: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 60: 60: [----------] 3 tests from BinAverageModuleTest 60: [ RUN ] BinAverageModuleTest.ComputesCorrectly 60: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 60: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 60: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 60: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 60: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 60: [----------] 3 tests from BinAverageModuleTest (0 ms total) 60: 60: [----------] 4 tests from AbstractAverageHistogramTest 60: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 60: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 60: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 60: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 60: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 60: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 60: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 60: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 60: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 60: 60: [----------] 3 tests from LifetimeModuleTest 60: [ RUN ] LifetimeModuleTest.BasicTest 60: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 60: [ RUN ] LifetimeModuleTest.CumulativeTest 60: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 60: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 60: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 60: [----------] 3 tests from LifetimeModuleTest (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 69 tests from 14 test suites ran. (14 ms total) 60: [ PASSED ] 69 tests. 60/96 Test #60: AnalysisDataUnitTests ........................ Passed 0.09 sec test 61 Start 61: CoordinateIOTests 61: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/coordinateio/tests 61: Test timeout computed to be: 30 61: [==========] Running 67 tests from 20 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from OutputSelectorDeathTest 61: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (1 ms) 61: [----------] 1 test from OutputSelectorDeathTest (1 ms total) 61: 61: [----------] 5 tests from TrajectoryFrameWriterTest 61: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 61: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 61: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 61: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 61: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 61: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 61: [----------] 5 tests from TrajectoryFrameWriterTest (4 ms total) 61: 61: [----------] 5 tests from OutputAdapterContainer 61: [ RUN ] OutputAdapterContainer.MakeEmpty 61: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 61: [ RUN ] OutputAdapterContainer.AddAdapter 61: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 61: [ RUN ] OutputAdapterContainer.RejectBadAdapter 61: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 61: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 61: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 61: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 61: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 61: [----------] 5 tests from OutputAdapterContainer (0 ms total) 61: 61: [----------] 3 tests from RegisterFrameConverterTest 61: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 61: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 61: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 61: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 61: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 61: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 61: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 61: 61: [----------] 5 tests from FlagTest 61: [ RUN ] FlagTest.CanSetSimpleFlag 61: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 61: [ RUN ] FlagTest.CanAddNewBox 61: [ OK ] FlagTest.CanAddNewBox (0 ms) 61: [ RUN ] FlagTest.SetsImplicitPrecisionChange 61: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 61: [ RUN ] FlagTest.SetsImplicitStartTimeChange 61: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 61: [ RUN ] FlagTest.SetsImplicitTimeStepChange 61: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 61: [----------] 5 tests from FlagTest (0 ms total) 61: 61: [----------] 5 tests from SetAtomsTest 61: [ RUN ] SetAtomsTest.RemovesExistingAtoms 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 61: [ RUN ] SetAtomsTest.AddsNewAtoms 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 61: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 61: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 61: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 61: [----------] 5 tests from SetAtomsTest (4 ms total) 61: 61: [----------] 2 tests from SetBothTimeTest 61: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 61: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 61: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 61: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 61: [----------] 2 tests from SetBothTimeTest (0 ms total) 61: 61: [----------] 2 tests from SetStartTimeTest 61: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 61: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 61: [ RUN ] SetStartTimeTest.WorksWithZeroStart 61: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 61: [----------] 2 tests from SetStartTimeTest (0 ms total) 61: 61: [----------] 1 test from SetTimeStepTest 61: [ RUN ] SetTimeStepTest.SetTimeStepWorks 61: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 61: [----------] 1 test from SetTimeStepTest (0 ms total) 61: 61: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 61: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 61: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (5 ms total) 61: 61: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) 61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 61: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 61: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (2 ms total) 61: 61: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 61: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 61: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 61: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 61: 61: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) 61: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 61: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (8 ms total) 61: 61: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 61: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 61: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 61: 61: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 61: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 61: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 61: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 61: 61: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 61: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 61: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 61: 61: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 61: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 61: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 61: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 61: 61: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 61: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 61: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 61: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (1 ms total) 61: 61: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 61: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 61: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 61: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 61: 61: [----------] 4 tests from ModuleSupported/NoOptionalOutput 61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 61: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 61: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 67 tests from 20 test suites ran. (38 ms total) 61: [ PASSED ] 67 tests. 61/96 Test #61: CoordinateIOTests ............................ Passed 0.16 sec test 62 Start 62: TrajectoryAnalysisUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests 62: Test timeout computed to be: 1920 62: [==========] Running 393 tests from 21 test suites. 62: [----------] Global test environment set-up. 62: [----------] 11 tests from AngleModuleTest 62: [ RUN ] AngleModuleTest.ComputesSimpleAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 62: [ RUN ] AngleModuleTest.ComputesDihedrals 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 62: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 62: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 62: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 62: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 62: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 62: Reading frames from gro file 'Test system for different angles', 33 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 62: [ RUN ] AngleModuleTest.ComputesMultipleAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 62: [ RUN ] AngleModuleTest.HandlesDynamicSelections 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 62: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 62: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 62: [----------] 11 tests from AngleModuleTest (15 ms total) 62: 62: [----------] 5 tests from ClustsizeTest 62: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 62: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 62: There is one group in the index 62: '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Total number of atoms in clusters = 24 62: cmid: 2, cmax: 4, max_size: 6 62: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 62: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (0 ms) 62: [ RUN ] ClustsizeTest.NoMolShortCutoff 62: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 62: There is one group in the index 62: '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Total number of atoms in clusters = 24 62: cmid: 1, cmax: 6, max_size: 6 62: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 62: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 62: [ RUN ] ClustsizeTest.MolDefaultCutoff 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Total number of atoms in clusters = 8 62: cmid: 2, cmax: 4, max_size: 2 62: 50%100%cmid: 2, cmax: 6, max_size: 2 62: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (0 ms) 62: [ RUN ] ClustsizeTest.MolShortCutoff 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Total number of atoms in clusters = 8 62: cmid: 1, cmax: 6, max_size: 2 62: 50%100%cmid: 2, cmax: 6, max_size: 2 62: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 62: [ RUN ] ClustsizeTest.MolCSize 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Total number of atoms in clusters = 8 62: cmid: 2, cmax: 4, max_size: 2 62: 50%100%cmid: 2, cmax: 6, max_size: 2 62: 50%100%[ OK ] ClustsizeTest.MolCSize (0 ms) 62: [----------] 5 tests from ClustsizeTest (5 ms total) 62: 62: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 62: Reading frames from gro file 'Test system', 8 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 62: Reading frames from gro file 'Test system', 8 atoms. 62: Reading frame 0 time 0.000 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 62: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 62: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 62: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 ms total) 62: 62: [----------] 4 tests from ConvertTrjModuleTest 62: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (5 ms) 62: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 62: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 62: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 62: Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 62: [----------] 4 tests from ConvertTrjModuleTest (12 ms total) 62: 62: [----------] 6 tests from DistanceModuleTest 62: [ RUN ] DistanceModuleTest.ComputesDistances 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: atomname S1 S2: 62: Number of samples: 5 62: Average distance: 1.43246 nm 62: Standard deviation: 0.96700 nm 62: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 62: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: atomname S1 S2: 62: Number of samples: 5 62: Average distance: 1.43246 nm 62: Standard deviation: 0.96700 nm 62: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 62: Number of samples: 4 62: Average distance: 1.81066 nm 62: Standard deviation: 0.79289 nm 62: [ OK ] DistanceModuleTest.ComputesMultipleDistances (2 ms) 62: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: atomname S1 S2 and res_cog x < 2.8: 62: Number of samples: 3 62: Average distance: 1.72076 nm 62: Standard deviation: 1.24839 nm 62: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 62: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: Contacts: 62: Number of samples: 2 62: Average distance: 1.00000 nm 62: Standard deviation: 0.00000 nm 62: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (3 ms) 62: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: SuccessiveContacts: 62: Number of samples: 2 62: Average distance: 1.00000 nm 62: Standard deviation: 0.00000 nm 62: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 62: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: ManyContacts: 62: Number of samples: 10 62: Average distance: 1.82913 nm 62: Standard deviation: 0.78478 nm 62: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) 62: [----------] 6 tests from DistanceModuleTest (17 ms total) 62: 62: [----------] 2 tests from ExtractClusterModuleTest 62: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 62: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 62: Analyzed 26 frames, last time 0.050 62: There are 8 clusters containing 26 structures, highest framenr is 25 62: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 62: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 62: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 62: Analyzed 26 frames, last time 0.050 62: There are 8 clusters containing 26 structures, highest framenr is 25 62: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 62: [----------] 2 tests from ExtractClusterModuleTest (2 ms total) 62: 62: [----------] 2 tests from FreeVolumeModuleTest 62: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for CO2-RM. Set to zero. 62: Could not determine VDW radius for 40 particles. These were set to zero. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: cutoff = 0.18 nm 62: probe_radius = 0 nm 62: seed = 13 62: ninsert = 1000 probes per nm^3 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 62: Spoel, Luciano T. Costa 62: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 62: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 62: Environ. Sci. Technol. (2013) 62: DOI: 10.1021/es4020986 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Free volume 38.02 +/- 0.00 % 62: Total volume 68.92 +/- 0.00 nm^3 62: Number of molecules 340 total mass 63491.38 Dalton 62: Average molar mass: 186.74 Dalton 62: Density rho: 1529.71 +/- 0.00 nm^3 62: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 62: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 62: Fractional free volume 0.194 +/- 0.000 62: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (44 ms) 62: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: cutoff = 0.18 nm 62: probe_radius = 0 nm 62: seed = 17 62: ninsert = 1000 probes per nm^3 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 62: Spoel, Luciano T. Costa 62: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 62: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 62: Environ. Sci. Technol. (2013) 62: DOI: 10.1021/es4020986 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Free volume 38.48 +/- 0.00 % 62: Total volume 68.92 +/- 0.00 nm^3 62: Number of molecules 340 total mass 63491.38 Dalton 62: Average molar mass: 186.74 Dalton 62: Density rho: 1529.71 +/- 0.00 nm^3 62: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 62: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 62: Fractional free volume 0.200 +/- 0.000 62: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (44 ms) 62: [----------] 2 tests from FreeVolumeModuleTest (89 ms total) 62: 62: [----------] 13 tests from MsdModuleTest 62: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 62: Analyzed 10 frames, last time 9.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 62: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 62: Analyzed 10 frames, last time 9.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 62: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 62: Analyzed 10 frames, last time 9.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 62: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 62: Analyzed 10 frames, last time 9.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 62: [ RUN ] MsdModuleTest.multipleGroupsWork 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to -1782580809 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.multipleGroupsWork (13 ms) 62: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 0.100 62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 62: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 62: Analyzed 21 frames, last time 2.000 62: Setting the LD random seed to -745681298 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (13 ms) 62: [ RUN ] MsdModuleTest.trestartLessThanDt 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1347956877 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.trestartLessThanDt (11 ms) 62: [ RUN ] MsdModuleTest.trestartGreaterThanDt 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to -287608835 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.trestartGreaterThanDt (13 ms) 62: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1073825027 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (11 ms) 62: [ RUN ] MsdModuleTest.molTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to -13647939 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.molTest (13 ms) 62: [ RUN ] MsdModuleTest.beginFit 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to -203424451 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.beginFit (13 ms) 62: [ RUN ] MsdModuleTest.endFit 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to 2112552542 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.endFit (13 ms) 62: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 1818.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 62: NVE simulation: will use the initial temperature of 288.764 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 62: There are 9 non-linear virtual site constructions. Their contribution to 62: the energy error is approximated. In most cases this does not affect the 62: error significantly. 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: NOTE: You provided an index file 62: /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 62: (with -n), but it was not used by any selection. 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 2.000 62: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 62: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 62: Analyzed 21 frames, last time 40.000 62: Setting the LD random seed to 1521472665 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 62: 62: Cleaning up constraints and constant bonded interactions with virtual sites 62: 62: Converted 15 Bonds with virtual sites to connections, 7 left 62: 62: Removed 18 Angles with virtual sites, 21 left 62: 62: Removed 10 Proper Dih.s with virtual sites, 44 left 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (13 ms) 62: [----------] 13 tests from MsdModuleTest (123 ms total) 62: 62: [----------] 9 tests from PairDistanceModuleTest 62: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 62: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 62: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 62: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 62: [----------] 9 tests from PairDistanceModuleTest (11 ms total) 62: 62: [----------] 5 tests from RdfModuleTest 62: [ RUN ] RdfModuleTest.BasicTest 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] RdfModuleTest.BasicTest (10 ms) 62: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 62: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (8 ms) 62: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (10 ms) 62: [ RUN ] RdfModuleTest.CalculatesSurf 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] RdfModuleTest.CalculatesSurf (4 ms) 62: [ RUN ] RdfModuleTest.CalculatesXY 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] RdfModuleTest.CalculatesXY (11 ms) 62: [----------] 5 tests from RdfModuleTest (46 ms total) 62: 62: [----------] 5 tests from SasaModuleTest 62: [ RUN ] SasaModuleTest.BasicTest 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 62: of Surface Area and Volume and to Dot Surface Contouring of Molecular 62: Assemblies 62: J. Comp. Chem. (1995) 62: DOI: 10.1002/jcc.540160303 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Analyzed topology coordinates 62: [ OK ] SasaModuleTest.BasicTest (5 ms) 62: [ RUN ] SasaModuleTest.HandlesSelectedResidues 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 62: of Surface Area and Volume and to Dot Surface Contouring of Molecular 62: Assemblies 62: J. Comp. Chem. (1995) 62: DOI: 10.1002/jcc.540160303 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Analyzed topology coordinates 62: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 62: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 62: of Surface Area and Volume and to Dot Surface Contouring of Molecular 62: Assemblies 62: J. Comp. Chem. (1995) 62: DOI: 10.1002/jcc.540160303 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Analyzed topology coordinates 62: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (2 ms) 62: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 62: of Surface Area and Volume and to Dot Surface Contouring of Molecular 62: Assemblies 62: J. Comp. Chem. (1995) 62: DOI: 10.1002/jcc.540160303 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Analyzed topology coordinates 62: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (4 ms) 62: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 62: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 62: of Surface Area and Volume and to Dot Surface Contouring of Molecular 62: Assemblies 62: J. Comp. Chem. (1995) 62: DOI: 10.1002/jcc.540160303 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 62: from the source below. This means the results may be different 62: compared to previous GROMACS versions. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: DOI: 10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Analyzed topology coordinates 62: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (3 ms) 62: [----------] 5 tests from SasaModuleTest (19 ms total) 62: 62: [----------] 8 tests from SelectModuleTest 62: [ RUN ] SelectModuleTest.BasicTest 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.BasicTest (2 ms) 62: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 62: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 62: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 62: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 62: [ RUN ] SelectModuleTest.NormalizesSizes 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 62: [ RUN ] SelectModuleTest.WritesResidueNumbers 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 62: [ RUN ] SelectModuleTest.WritesResidueIndices 62: Analyzed topology coordinates 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 62: [----------] 8 tests from SelectModuleTest (12 ms total) 62: 62: [----------] 10 tests from SurfaceAreaTest 62: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 62: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 62: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 62: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 62: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 62: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 62: [ RUN ] SurfaceAreaTest.SurfacePoints12 62: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 62: [ RUN ] SurfaceAreaTest.SurfacePoints32 62: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 62: [ RUN ] SurfaceAreaTest.SurfacePoints42 62: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 62: [ RUN ] SurfaceAreaTest.SurfacePoints122 62: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 62: [ RUN ] SurfaceAreaTest.Computes100Points 62: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 62: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 62: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 62: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 62: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 62: [----------] 10 tests from SurfaceAreaTest (4 ms total) 62: 62: [----------] 4 tests from TopologyInformation 62: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 62: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 62: [ RUN ] TopologyInformation.WorksWithGroFile 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TopologyInformation.WorksWithGroFile (0 ms) 62: [ RUN ] TopologyInformation.WorksWithPdbFile 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 62: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 62: Setting the LD random seed to -29364361 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (171 ms) 62: [----------] 4 tests from TopologyInformation (173 ms total) 62: 62: [----------] 4 tests from TrajectoryModuleTest 62: [ RUN ] TrajectoryModuleTest.BasicTest 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 62: [ RUN ] TrajectoryModuleTest.PlotsXOnly 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 62: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 62: [ RUN ] TrajectoryModuleTest.HandlesNoForces 62: Reading frames from gro file 'Test system', 15 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 62: Analyzed 2 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 62: [----------] 4 tests from TrajectoryModuleTest (5 ms total) 62: 62: [----------] 5 tests from UnionFinderTest 62: [ RUN ] UnionFinderTest.WorksEmpty 62: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 62: [ RUN ] UnionFinderTest.BasicMerges 62: [ OK ] UnionFinderTest.BasicMerges (0 ms) 62: [ RUN ] UnionFinderTest.LargerMerges 62: [ OK ] UnionFinderTest.LargerMerges (0 ms) 62: [ RUN ] UnionFinderTest.LongRightMerge 62: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 62: [ RUN ] UnionFinderTest.LongLeftMerge 62: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 62: [----------] 5 tests from UnionFinderTest (0 ms total) 62: 62: [----------] 1 test from MappedUnionFinderTest 62: [ RUN ] MappedUnionFinderTest.BasicMerges 62: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 62: [----------] 1 test from MappedUnionFinderTest (0 ms total) 62: 62: [----------] 192 tests from MoleculeTests/DsspModuleTest 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (10 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (11 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (12 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (9 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (8 ms) 62: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 62: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 62: Last frame 0 time 500.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: W. Kabsch, C. Sander 62: Dictionary of protein secondary structure: pattern recognition of 62: hydrogen-bonded and geometrical features 62: Biopolymers (1983) 62: DOI: 10.1002/bip.360221211 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 62: Trajectories 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c01344 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (8 ms) 62: [----------] 192 tests from MoleculeTests/DsspModuleTest (2061 ms total) 62: 62: [----------] 3 tests from GyrateTests/GyrateModuleTest 62: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (4 ms) 62: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (4 ms) 62: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) 62: [----------] 3 tests from GyrateTests/GyrateModuleTest (13 ms total) 62: 62: [----------] 96 tests from HBondTests/HbondModuleTest 62: [ RUN ] HBondTests/HbondModuleTest.Works/0 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/0 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/1 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/1 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/2 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/2 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/3 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/3 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/4 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/4 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/5 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/5 (8 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/6 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/6 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/7 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/7 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/8 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/8 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/9 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/9 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/10 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/10 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/11 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/11 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/12 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/12 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/13 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/13 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/14 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/14 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/15 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/15 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/16 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/16 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/17 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/17 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/18 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/18 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/19 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/19 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/20 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/20 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/21 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/21 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/22 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/22 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/23 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/23 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/24 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/24 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/25 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/25 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/26 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/26 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/27 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/27 (6 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/28 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/28 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/29 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/29 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/30 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/30 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/31 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/31 (7 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/32 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/32 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/33 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/33 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/34 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/34 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/35 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/35 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/36 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/36 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/37 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/37 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/38 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/38 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/39 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/39 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/40 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/40 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/41 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/41 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/42 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/42 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/43 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/43 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/44 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/44 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/45 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/45 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/46 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/46 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/47 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/47 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/48 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/48 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/49 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/49 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/50 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/50 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/51 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/51 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/52 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/52 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/53 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/53 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/54 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/54 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/55 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/55 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/56 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/56 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/57 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/57 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/58 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/58 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/59 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/59 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/60 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/60 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/61 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 27 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/61 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/62 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 56 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/62 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/63 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 62: Selection 'Protein' has 29 acceptors and 4 donors. 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Merging hbonds with Acceptor and Donor swapped 62: [ OK ] HBondTests/HbondModuleTest.Works/63 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/64 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/64 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/65 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/65 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/66 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/66 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/67 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/67 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/68 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/68 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/69 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/69 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/70 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/70 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/71 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/71 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/72 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/72 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/73 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/73 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/74 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/74 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/75 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/75 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/76 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/76 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/77 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/77 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/78 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/78 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/79 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/79 (41 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/80 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/80 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/81 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/81 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/82 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/82 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/83 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/83 (37 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/84 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/84 (47 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/85 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/85 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/86 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/86 (38 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/87 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/87 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/88 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/88 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/89 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/89 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/90 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/90 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/91 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/91 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/92 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/92 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/93 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/93 (39 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/94 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/94 (40 ms) 62: [ RUN ] HBondTests/HbondModuleTest.Works/95 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 62: Analyzed 2 frames, last time 10.000 62: 62: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 62: Selection 'Water' has 1160 acceptors and 1160 donors. 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 62: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 62: Memory Limitation 62: Journal of Chemical Information and Modeling (2024) 62: DOI: 10.1021/acs.jcim.3c02087 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] HBondTests/HbondModuleTest.Works/95 (40 ms) 62: [----------] 96 tests from HBondTests/HbondModuleTest (3158 ms total) 62: 62: [----------] 4 tests from MoleculeTests/ScatteringModule 62: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 62: Method for calculating small-angle neutron scattering spectra using all-atom 62: molecular dynamics trajectories 62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 62: DOI: 10.1134/S1027451013060372 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) 62: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 62: Method for calculating small-angle neutron scattering spectra using all-atom 62: molecular dynamics trajectories 62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 62: DOI: 10.1134/S1027451013060372 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: D. T. Cromer, J. B. Mann 62: X-ray scattering factors computed from numerical Hartree-Fock wave functions 62: Acta Cryst. A (1968) 62: DOI: 10.1107/S0567739468000550 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (161 ms) 62: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 62: Method for calculating small-angle neutron scattering spectra using all-atom 62: molecular dynamics trajectories 62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 62: DOI: 10.1134/S1027451013060372 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 62: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 62: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 62: Last frame 0 time 0.000 62: Analyzed 1 frames, last time 0.000 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 62: Method for calculating small-angle neutron scattering spectra using all-atom 62: molecular dynamics trajectories 62: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 62: DOI: 10.1134/S1027451013060372 62: -------- -------- --- Thank You --- -------- -------- 62: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: D. T. Cromer, J. B. Mann 62: X-ray scattering factors computed from numerical Hartree-Fock wave functions 62: Acta Cryst. A (1968) 62: DOI: 10.1107/S0567739468000550 62: -------- -------- --- Thank You --- -------- -------- 62: 62: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (37 ms) 62: [----------] 4 tests from MoleculeTests/ScatteringModule (212 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 393 tests from 21 test suites ran. (5990 ms total) 62: [ PASSED ] 393 tests. 62/96 Test #62: TrajectoryAnalysisUnitTests .................. Passed 6.15 sec test 63 Start 63: EnergyAnalysisUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis/tests 63: Test timeout computed to be: 30 63: [==========] Running 12 tests from 5 test suites. 63: [----------] Global test environment set-up. 63: [----------] 2 tests from EnergyTermTest 63: [ RUN ] EnergyTermTest.ConstructWorks 63: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 63: [ RUN ] EnergyTermTest.AddFrameWorks 63: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 63: [----------] 2 tests from EnergyTermTest (0 ms total) 63: 63: [----------] 1 test from DhdlTest 63: [ RUN ] DhdlTest.ExtractDhdl 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 63: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 63: Note: file tpx version 110, software tpx version 137 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 63: 63: 63: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 63: [ OK ] DhdlTest.ExtractDhdl (4 ms) 63: [----------] 1 test from DhdlTest (5 ms total) 63: 63: [----------] 1 test from OriresTest 63: [ RUN ] OriresTest.ExtractOrires 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 63: Reading file /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 63: Note: file tpx version 111, software tpx version 137 63: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 63: End your selection with 0 63: Selecting all 7 orientation restraints 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 63: [ OK ] OriresTest.ExtractOrires (6 ms) 63: [----------] 1 test from OriresTest (6 ms total) 63: 63: [----------] 5 tests from EnergyTest 63: [ RUN ] EnergyTest.ExtractEnergy 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: 63: Select the terms you want from the following list by 63: selecting either (part of) the name or the number or a combination. 63: End your selection with an empty line or a zero. 63: ------------------------------------------------------------------- 63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 63: 13 Box-Z 14 Volume 15 Density 16 pV 63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 63: 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 63: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 63: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 63: [ OK ] EnergyTest.ExtractEnergy (1 ms) 63: [ RUN ] EnergyTest.ExtractEnergyByNumber 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: 63: Select the terms you want from the following list by 63: selecting either (part of) the name or the number or a combination. 63: End your selection with an empty line or a zero. 63: ------------------------------------------------------------------- 63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 63: 13 Box-Z 14 Volume 15 Density 16 pV 63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 63: 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 63: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 63: Pres. DC -268.49 3 8.52175 13.2804 (bar) 63: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 63: [ RUN ] EnergyTest.ExtractEnergyMixed 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: 63: Select the terms you want from the following list by 63: selecting either (part of) the name or the number or a combination. 63: End your selection with an empty line or a zero. 63: ------------------------------------------------------------------- 63: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 63: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 63: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 63: 13 Box-Z 14 Volume 15 Density 16 pV 63: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 63: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 63: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 63: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 63: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 63: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 63: 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 63: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 63: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 63: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 63: 63: Select the terms you want from the following list by 63: selecting either (part of) the name or the number or a combination. 63: End your selection with an empty line or a zero. 63: ------------------------------------------------------------------- 63: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 63: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 63: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 63: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 63: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 63: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 63: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 63: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 63: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 63: 37 1/Viscosity 38 T-System 39 Lamb-System 63: 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 63: 63: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 63: All statistics are over 3 points (frames) 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 63: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 63: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 63: 63: Select the terms you want from the following list by 63: selecting either (part of) the name or the number or a combination. 63: End your selection with an empty line or a zero. 63: ------------------------------------------------------------------- 63: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 63: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 63: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 63: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 63: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 63: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 63: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 63: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 63: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 63: 37 1/Viscosity 38 T-System 39 Lamb-System 63: 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 63: 63: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 63: All statistics are over 3 points (frames) 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 63: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 63: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 63: [----------] 5 tests from EnergyTest (5 ms total) 63: 63: [----------] 3 tests from ViscosityTest 63: [ RUN ] ViscosityTest.EinsteinViscosity 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Pres-XX 20.2092 65 717.193 185.978 (bar) 63: Pres-XY -47.7351 39 372.522 207.456 (bar) 63: Pres-XZ 11.477 31 379.79 6.80818 (bar) 63: Pres-YX -47.7106 39 372.525 207.5 (bar) 63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 63: Pres-YZ -41.3534 45 401.216 114.663 (bar) 63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 63: Pres-ZY -41.3119 45 401.196 114.743 (bar) 63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 63: 63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 63: [ OK ] ViscosityTest.EinsteinViscosity (167 ms) 63: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Pres-XX 20.2092 65 717.193 185.978 (bar) 63: Pres-XY -47.7351 39 372.522 207.456 (bar) 63: Pres-XZ 11.477 31 379.79 6.80818 (bar) 63: Pres-YX -47.7106 39 372.525 207.5 (bar) 63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 63: Pres-YZ -41.3534 45 401.216 114.663 (bar) 63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 63: Pres-ZY -41.3119 45 401.196 114.743 (bar) 63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 63: 63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 63: [ OK ] ViscosityTest.EinsteinViscosityIntegral (109 ms) 63: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 63: Opened /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 63: 63: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 63: All statistics are over 5001 points 63: 63: Energy Average Err.Est. RMSD Tot-Drift 63: ------------------------------------------------------------------------------- 63: Pres-XX 20.2092 65 717.193 185.978 (bar) 63: Pres-XY -47.7351 39 372.522 207.456 (bar) 63: Pres-XZ 11.477 31 379.79 6.80818 (bar) 63: Pres-YX -47.7106 39 372.525 207.5 (bar) 63: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 63: Pres-YZ -41.3534 45 401.216 114.663 (bar) 63: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 63: Pres-ZY -41.3119 45 401.196 114.743 (bar) 63: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 63: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 63: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 63: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 63: 63: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 63: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (103 ms) 63: [----------] 3 tests from ViscosityTest (380 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 12 tests from 5 test suites ran. (396 ms total) 63: [ PASSED ] 12 tests. 63/96 Test #63: EnergyAnalysisUnitTests ...................... Passed 0.69 sec test 64 Start 64: ToolUnitTests 64: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/ToolUnitTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests 64: Test timeout computed to be: 1920 64: [==========] Running 63 tests from 8 test suites. 64: [----------] Global test environment set-up. 64: [----------] 2 tests from DumpTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Setting the LD random seed to -584518409 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: [ RUN ] DumpTest.WorksWithTpr 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 64: inputrec: 64: integrator = md 64: tinit = 0 64: dt = 0.001 64: nsteps = 0 64: init-step = 0 64: simulation-part = 1 64: mts = false 64: mass-repartition-factor = 1 64: comm-mode = Linear 64: nstcomm = 100 64: bd-fric = 0 64: ld-seed = -584518409 64: emtol = 10 64: emstep = 0.01 64: niter = 20 64: fcstep = 0 64: nstcgsteep = 1000 64: nbfgscorr = 10 64: rtpi = 0.05 64: nstxout = 0 64: nstvout = 0 64: nstfout = 0 64: nstlog = 1000 64: nstcalcenergy = 100 64: nstenergy = 1000 64: nstxout-compressed = 0 64: compressed-x-precision = 1000 64: cutoff-scheme = Verlet 64: nstlist = 10 64: pbc = xyz 64: periodic-molecules = false 64: verlet-buffer-tolerance = -1 64: verlet-buffer-pressure-tolerance = 0.5 64: rlist = 1.1 64: coulombtype = Cut-off 64: coulomb-modifier = Potential-shift 64: rcoulomb-switch = 0 64: rcoulomb = 1 64: epsilon-r = 1 64: epsilon-rf = inf 64: vdw-type = Cut-off 64: vdw-modifier = Potential-shift 64: rvdw-switch = 0 64: rvdw = 1 64: DispCorr = No 64: table-extension = 1 64: fourierspacing = 0.12 64: fourier-nx = 0 64: fourier-ny = 0 64: fourier-nz = 0 64: pme-order = 4 64: ewald-rtol = 1e-05 64: ewald-rtol-lj = 0.001 64: lj-pme-comb-rule = Geometric 64: ewald-geometry = 3d 64: epsilon-surface = 0 64: ensemble-temperature-setting = not available 64: tcoupl = No 64: nsttcouple = -1 64: nh-chain-length = 0 64: print-nose-hoover-chain-variables = false 64: pcoupl = No 64: refcoord-scaling = No 64: posres-com: not available 64: posres-comB: not available 64: QMMM = false 64: qm-opts: 64: ngQM = 0 64: constraint-algorithm = Lincs 64: continuation = false 64: Shake-SOR = false 64: shake-tol = 0.0001 64: lincs-order = 4 64: lincs-iter = 1 64: lincs-warnangle = 30 64: nwall = 0 64: wall-type = 9-3 64: wall-r-linpot = -1 64: wall-atomtype[0] = -1 64: wall-atomtype[1] = -1 64: wall-density[0] = 0 64: wall-density[1] = 0 64: wall-ewald-zfac = 3 64: pull = false 64: awh = false 64: rotation = false 64: interactiveMD = false 64: disre = No 64: disre-weighting = Conservative 64: disre-mixed = false 64: dr-fc = 1000 64: dr-tau = 0 64: nstdisreout = 100 64: orire-fc = 0 64: orire-tau = 0 64: nstorireout = 100 64: free-energy = no 64: cos-acceleration = 0 64: deform (3x3): 64: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: simulated-tempering = false 64: swapcoords = no 64: userint1 = 0 64: userint2 = 0 64: userint3 = 0 64: userint4 = 0 64: userreal1 = 0 64: userreal2 = 0 64: userreal3 = 0 64: userreal4 = 0 64: applied-forces: 64: electric-field: 64: x: 64: E0 = 0 64: omega = 0 64: t0 = 0 64: sigma = 0 64: y: 64: E0 = 0 64: omega = 0 64: t0 = 0 64: sigma = 0 64: z: 64: E0 = 0 64: omega = 0 64: t0 = 0 64: sigma = 0 64: density-guided-simulation: 64: active = false 64: group = protein 64: similarity-measure = inner-product 64: atom-spreading-weight = unity 64: force-constant = 1e+09 64: gaussian-transform-spreading-width = 0.2 64: gaussian-transform-spreading-range-in-multiples-of-width = 4 64: reference-density-filename = reference.mrc 64: nst = 1 64: normalize-densities = true 64: adaptive-force-scaling = false 64: adaptive-force-scaling-time-constant = 4 64: shift-vector = 64: transformation-matrix = 64: qmmm-cp2k: 64: active = false 64: qmgroup = System 64: qmmethod = PBE 64: qmfilenames = 64: qmcharge = 0 64: qmmultiplicity = 1 64: colvars: 64: active = false 64: configfile = 64: seed = -1 64: nnpot: 64: active = false 64: modelfile = model.pt 64: input-group = System 64: model-input1 = 64: model-input2 = 64: model-input3 = 64: model-input4 = 64: grpopts: 64: nrdf: 465 64: ref-t: 0 64: tau-t: 0 64: annealing: No 64: annealing-npoints: 0 64: acc: 0 0 0 64: nfreeze: N N N 64: energygrp-flags[ 0]: 0 64: header: 64: bIr = present 64: bBox = present 64: bTop = present 64: bX = present 64: bV = present 64: bF = not present 64: natoms = 156 64: lambda = 0.000000e+00 64: buffer size = 46382 64: topology: 64: name="First 10 residues from 1AKI" 64: #atoms = 156 64: #molblock = 1 64: molblock (0): 64: moltype = 0 "Protein_chain_B" 64: #molecules = 1 64: #posres_xA = 0 64: #posres_xB = 0 64: bIntermolecularInteractions = false 64: ffparams: 64: atnr=10 64: ntypes=212 64: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 64: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 64: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 64: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 64: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 64: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 64: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 64: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 64: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 64: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 64: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 64: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 64: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 64: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 64: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 64: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 64: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 64: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 64: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 64: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 64: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 64: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 64: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 64: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 64: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 64: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 64: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 64: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 64: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 64: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 64: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 64: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 64: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 64: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 64: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 64: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 64: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 64: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 64: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 64: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 64: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 64: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 64: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 64: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 64: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 64: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 64: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 64: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 64: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 64: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 64: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 64: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 64: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 64: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 64: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 64: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 64: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 64: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 64: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 64: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 64: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 64: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 64: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 64: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 64: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 64: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 64: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 64: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 64: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 64: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 64: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 64: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 64: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 64: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 64: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 64: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 64: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 64: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 64: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 64: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 64: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 64: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 64: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 64: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 64: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 64: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 64: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 64: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 64: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 64: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 64: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 64: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 64: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 64: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 64: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 64: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 64: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 64: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 64: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 64: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 64: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 64: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 64: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 64: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 64: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 64: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 64: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 64: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 64: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 64: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 64: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 64: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 64: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 64: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 64: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 64: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 64: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 64: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 64: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 64: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 64: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 64: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 64: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 64: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 64: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 64: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 64: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 64: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 64: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 64: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 64: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 64: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 64: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 64: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 64: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 64: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 64: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 64: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 64: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 64: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 64: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 64: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 64: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 64: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 64: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 64: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 64: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 64: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 64: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 64: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 64: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 64: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 64: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 64: reppow = 12 64: fudgeQQ = 0.5 64: cmap 64: moltype (0): 64: name="Protein_chain_B" 64: atoms: 64: atom (156): 64: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 64: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 64: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 64: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 64: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 64: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 64: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 64: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 64: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 64: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 64: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 64: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 64: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 64: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 64: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 64: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 64: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 64: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 64: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 64: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 64: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 64: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 64: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 64: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 64: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 64: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 64: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 64: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 64: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 64: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 64: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 64: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 64: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 64: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 64: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 64: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 64: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 64: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 64: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 64: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 64: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 64: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 64: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 64: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 64: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 64: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 64: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 64: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 64: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 64: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 64: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 64: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 64: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 64: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 64: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 64: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 64: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 64: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 64: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 64: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 64: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 64: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 64: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 64: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 64: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 64: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 64: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 64: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 64: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 64: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 64: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 64: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 64: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 64: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 64: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 64: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 64: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 64: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 64: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 64: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 64: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 64: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 64: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 64: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 64: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 64: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 64: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 64: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 64: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 64: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 64: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 64: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 64: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 64: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 64: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 64: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 64: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 64: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 64: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 64: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 64: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 64: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 64: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 64: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 64: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 64: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 64: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 64: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 64: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 64: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 64: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 64: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 64: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 64: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 64: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 64: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 64: atom (156): 64: atom[0]={name="N"} 64: atom[1]={name="H1"} 64: atom[2]={name="H2"} 64: atom[3]={name="H3"} 64: atom[4]={name="CA"} 64: atom[5]={name="HA"} 64: atom[6]={name="CB"} 64: atom[7]={name="HB1"} 64: atom[8]={name="HB2"} 64: atom[9]={name="CG"} 64: atom[10]={name="HG1"} 64: atom[11]={name="HG2"} 64: atom[12]={name="CD"} 64: atom[13]={name="HD1"} 64: atom[14]={name="HD2"} 64: atom[15]={name="CE"} 64: atom[16]={name="HE1"} 64: atom[17]={name="HE2"} 64: atom[18]={name="NZ"} 64: atom[19]={name="HZ1"} 64: atom[20]={name="HZ2"} 64: atom[21]={name="HZ3"} 64: atom[22]={name="C"} 64: atom[23]={name="O"} 64: atom[24]={name="N"} 64: atom[25]={name="H"} 64: atom[26]={name="CA"} 64: atom[27]={name="HA"} 64: atom[28]={name="CB"} 64: atom[29]={name="HB"} 64: atom[30]={name="CG1"} 64: atom[31]={name="HG11"} 64: atom[32]={name="HG12"} 64: atom[33]={name="HG13"} 64: atom[34]={name="CG2"} 64: atom[35]={name="HG21"} 64: atom[36]={name="HG22"} 64: atom[37]={name="HG23"} 64: atom[38]={name="C"} 64: atom[39]={name="O"} 64: atom[40]={name="N"} 64: atom[41]={name="H"} 64: atom[42]={name="CA"} 64: atom[43]={name="HA"} 64: atom[44]={name="CB"} 64: atom[45]={name="HB1"} 64: atom[46]={name="HB2"} 64: atom[47]={name="CG"} 64: atom[48]={name="CD1"} 64: atom[49]={name="HD1"} 64: atom[50]={name="CD2"} 64: atom[51]={name="HD2"} 64: atom[52]={name="CE1"} 64: atom[53]={name="HE1"} 64: atom[54]={name="CE2"} 64: atom[55]={name="HE2"} 64: atom[56]={name="CZ"} 64: atom[57]={name="HZ"} 64: atom[58]={name="C"} 64: atom[59]={name="O"} 64: atom[60]={name="N"} 64: atom[61]={name="H"} 64: atom[62]={name="CA"} 64: atom[63]={name="HA1"} 64: atom[64]={name="HA2"} 64: atom[65]={name="C"} 64: atom[66]={name="O"} 64: atom[67]={name="N"} 64: atom[68]={name="H"} 64: atom[69]={name="CA"} 64: atom[70]={name="HA"} 64: atom[71]={name="CB"} 64: atom[72]={name="HB1"} 64: atom[73]={name="HB2"} 64: atom[74]={name="CG"} 64: atom[75]={name="HG1"} 64: atom[76]={name="HG2"} 64: atom[77]={name="CD"} 64: atom[78]={name="HD1"} 64: atom[79]={name="HD2"} 64: atom[80]={name="NE"} 64: atom[81]={name="HE"} 64: atom[82]={name="CZ"} 64: atom[83]={name="NH1"} 64: atom[84]={name="HH11"} 64: atom[85]={name="HH12"} 64: atom[86]={name="NH2"} 64: atom[87]={name="HH21"} 64: atom[88]={name="HH22"} 64: atom[89]={name="C"} 64: atom[90]={name="O"} 64: atom[91]={name="N"} 64: atom[92]={name="H"} 64: atom[93]={name="CA"} 64: atom[94]={name="HA"} 64: atom[95]={name="CB"} 64: atom[96]={name="HB1"} 64: atom[97]={name="HB2"} 64: atom[98]={name="SG"} 64: atom[99]={name="HG"} 64: atom[100]={name="C"} 64: atom[101]={name="O"} 64: atom[102]={name="N"} 64: atom[103]={name="H"} 64: atom[104]={name="CA"} 64: atom[105]={name="HA"} 64: atom[106]={name="CB"} 64: atom[107]={name="HB1"} 64: atom[108]={name="HB2"} 64: atom[109]={name="CG"} 64: atom[110]={name="HG1"} 64: atom[111]={name="HG2"} 64: atom[112]={name="CD"} 64: atom[113]={name="OE1"} 64: atom[114]={name="OE2"} 64: atom[115]={name="C"} 64: atom[116]={name="O"} 64: atom[117]={name="N"} 64: atom[118]={name="H"} 64: atom[119]={name="CA"} 64: atom[120]={name="HA"} 64: atom[121]={name="CB"} 64: atom[122]={name="HB1"} 64: atom[123]={name="HB2"} 64: atom[124]={name="CG"} 64: atom[125]={name="HG"} 64: atom[126]={name="CD1"} 64: atom[127]={name="HD11"} 64: atom[128]={name="HD12"} 64: atom[129]={name="HD13"} 64: atom[130]={name="CD2"} 64: atom[131]={name="HD21"} 64: atom[132]={name="HD22"} 64: atom[133]={name="HD23"} 64: atom[134]={name="C"} 64: atom[135]={name="O"} 64: atom[136]={name="N"} 64: atom[137]={name="H"} 64: atom[138]={name="CA"} 64: atom[139]={name="HA"} 64: atom[140]={name="CB"} 64: atom[141]={name="HB1"} 64: atom[142]={name="HB2"} 64: atom[143]={name="HB3"} 64: atom[144]={name="C"} 64: atom[145]={name="O"} 64: atom[146]={name="N"} 64: atom[147]={name="H"} 64: atom[148]={name="CA"} 64: atom[149]={name="HA"} 64: atom[150]={name="CB"} 64: atom[151]={name="HB1"} 64: atom[152]={name="HB2"} 64: atom[153]={name="HB3"} 64: atom[154]={name="C"} 64: atom[155]={name="O"} 64: type (156): 64: type[0]={name="opls_287",nameB="opls_287"} 64: type[1]={name="opls_290",nameB="opls_290"} 64: type[2]={name="opls_290",nameB="opls_290"} 64: type[3]={name="opls_290",nameB="opls_290"} 64: type[4]={name="opls_293B",nameB="opls_293B"} 64: type[5]={name="opls_140",nameB="opls_140"} 64: type[6]={name="opls_136",nameB="opls_136"} 64: type[7]={name="opls_140",nameB="opls_140"} 64: type[8]={name="opls_140",nameB="opls_140"} 64: type[9]={name="opls_136",nameB="opls_136"} 64: type[10]={name="opls_140",nameB="opls_140"} 64: type[11]={name="opls_140",nameB="opls_140"} 64: type[12]={name="opls_136",nameB="opls_136"} 64: type[13]={name="opls_140",nameB="opls_140"} 64: type[14]={name="opls_140",nameB="opls_140"} 64: type[15]={name="opls_292",nameB="opls_292"} 64: type[16]={name="opls_140",nameB="opls_140"} 64: type[17]={name="opls_140",nameB="opls_140"} 64: type[18]={name="opls_287",nameB="opls_287"} 64: type[19]={name="opls_290",nameB="opls_290"} 64: type[20]={name="opls_290",nameB="opls_290"} 64: type[21]={name="opls_290",nameB="opls_290"} 64: type[22]={name="opls_235",nameB="opls_235"} 64: type[23]={name="opls_236",nameB="opls_236"} 64: type[24]={name="opls_238",nameB="opls_238"} 64: type[25]={name="opls_241",nameB="opls_241"} 64: type[26]={name="opls_224B",nameB="opls_224B"} 64: type[27]={name="opls_140",nameB="opls_140"} 64: type[28]={name="opls_137",nameB="opls_137"} 64: type[29]={name="opls_140",nameB="opls_140"} 64: type[30]={name="opls_135",nameB="opls_135"} 64: type[31]={name="opls_140",nameB="opls_140"} 64: type[32]={name="opls_140",nameB="opls_140"} 64: type[33]={name="opls_140",nameB="opls_140"} 64: type[34]={name="opls_135",nameB="opls_135"} 64: type[35]={name="opls_140",nameB="opls_140"} 64: type[36]={name="opls_140",nameB="opls_140"} 64: type[37]={name="opls_140",nameB="opls_140"} 64: type[38]={name="opls_235",nameB="opls_235"} 64: type[39]={name="opls_236",nameB="opls_236"} 64: type[40]={name="opls_238",nameB="opls_238"} 64: type[41]={name="opls_241",nameB="opls_241"} 64: type[42]={name="opls_224B",nameB="opls_224B"} 64: type[43]={name="opls_140",nameB="opls_140"} 64: type[44]={name="opls_149",nameB="opls_149"} 64: type[45]={name="opls_140",nameB="opls_140"} 64: type[46]={name="opls_140",nameB="opls_140"} 64: type[47]={name="opls_145",nameB="opls_145"} 64: type[48]={name="opls_145",nameB="opls_145"} 64: type[49]={name="opls_146",nameB="opls_146"} 64: type[50]={name="opls_145",nameB="opls_145"} 64: type[51]={name="opls_146",nameB="opls_146"} 64: type[52]={name="opls_145",nameB="opls_145"} 64: type[53]={name="opls_146",nameB="opls_146"} 64: type[54]={name="opls_145",nameB="opls_145"} 64: type[55]={name="opls_146",nameB="opls_146"} 64: type[56]={name="opls_145",nameB="opls_145"} 64: type[57]={name="opls_146",nameB="opls_146"} 64: type[58]={name="opls_235",nameB="opls_235"} 64: type[59]={name="opls_236",nameB="opls_236"} 64: type[60]={name="opls_238",nameB="opls_238"} 64: type[61]={name="opls_241",nameB="opls_241"} 64: type[62]={name="opls_223B",nameB="opls_223B"} 64: type[63]={name="opls_140",nameB="opls_140"} 64: type[64]={name="opls_140",nameB="opls_140"} 64: type[65]={name="opls_235",nameB="opls_235"} 64: type[66]={name="opls_236",nameB="opls_236"} 64: type[67]={name="opls_238",nameB="opls_238"} 64: type[68]={name="opls_241",nameB="opls_241"} 64: type[69]={name="opls_224B",nameB="opls_224B"} 64: type[70]={name="opls_140",nameB="opls_140"} 64: type[71]={name="opls_136",nameB="opls_136"} 64: type[72]={name="opls_140",nameB="opls_140"} 64: type[73]={name="opls_140",nameB="opls_140"} 64: type[74]={name="opls_308",nameB="opls_308"} 64: type[75]={name="opls_140",nameB="opls_140"} 64: type[76]={name="opls_140",nameB="opls_140"} 64: type[77]={name="opls_307",nameB="opls_307"} 64: type[78]={name="opls_140",nameB="opls_140"} 64: type[79]={name="opls_140",nameB="opls_140"} 64: type[80]={name="opls_303",nameB="opls_303"} 64: type[81]={name="opls_304",nameB="opls_304"} 64: type[82]={name="opls_302",nameB="opls_302"} 64: type[83]={name="opls_300",nameB="opls_300"} 64: type[84]={name="opls_301",nameB="opls_301"} 64: type[85]={name="opls_301",nameB="opls_301"} 64: type[86]={name="opls_300",nameB="opls_300"} 64: type[87]={name="opls_301",nameB="opls_301"} 64: type[88]={name="opls_301",nameB="opls_301"} 64: type[89]={name="opls_235",nameB="opls_235"} 64: type[90]={name="opls_236",nameB="opls_236"} 64: type[91]={name="opls_238",nameB="opls_238"} 64: type[92]={name="opls_241",nameB="opls_241"} 64: type[93]={name="opls_224B",nameB="opls_224B"} 64: type[94]={name="opls_140",nameB="opls_140"} 64: type[95]={name="opls_206",nameB="opls_206"} 64: type[96]={name="opls_140",nameB="opls_140"} 64: type[97]={name="opls_140",nameB="opls_140"} 64: type[98]={name="opls_200",nameB="opls_200"} 64: type[99]={name="opls_204",nameB="opls_204"} 64: type[100]={name="opls_235",nameB="opls_235"} 64: type[101]={name="opls_236",nameB="opls_236"} 64: type[102]={name="opls_238",nameB="opls_238"} 64: type[103]={name="opls_241",nameB="opls_241"} 64: type[104]={name="opls_224B",nameB="opls_224B"} 64: type[105]={name="opls_140",nameB="opls_140"} 64: type[106]={name="opls_136",nameB="opls_136"} 64: type[107]={name="opls_140",nameB="opls_140"} 64: type[108]={name="opls_140",nameB="opls_140"} 64: type[109]={name="opls_274",nameB="opls_274"} 64: type[110]={name="opls_140",nameB="opls_140"} 64: type[111]={name="opls_140",nameB="opls_140"} 64: type[112]={name="opls_271",nameB="opls_271"} 64: type[113]={name="opls_272",nameB="opls_272"} 64: type[114]={name="opls_272",nameB="opls_272"} 64: type[115]={name="opls_235",nameB="opls_235"} 64: type[116]={name="opls_236",nameB="opls_236"} 64: type[117]={name="opls_238",nameB="opls_238"} 64: type[118]={name="opls_241",nameB="opls_241"} 64: type[119]={name="opls_224B",nameB="opls_224B"} 64: type[120]={name="opls_140",nameB="opls_140"} 64: type[121]={name="opls_136",nameB="opls_136"} 64: type[122]={name="opls_140",nameB="opls_140"} 64: type[123]={name="opls_140",nameB="opls_140"} 64: type[124]={name="opls_137",nameB="opls_137"} 64: type[125]={name="opls_140",nameB="opls_140"} 64: type[126]={name="opls_135",nameB="opls_135"} 64: type[127]={name="opls_140",nameB="opls_140"} 64: type[128]={name="opls_140",nameB="opls_140"} 64: type[129]={name="opls_140",nameB="opls_140"} 64: type[130]={name="opls_135",nameB="opls_135"} 64: type[131]={name="opls_140",nameB="opls_140"} 64: type[132]={name="opls_140",nameB="opls_140"} 64: type[133]={name="opls_140",nameB="opls_140"} 64: type[134]={name="opls_235",nameB="opls_235"} 64: type[135]={name="opls_236",nameB="opls_236"} 64: type[136]={name="opls_238",nameB="opls_238"} 64: type[137]={name="opls_241",nameB="opls_241"} 64: type[138]={name="opls_224B",nameB="opls_224B"} 64: type[139]={name="opls_140",nameB="opls_140"} 64: type[140]={name="opls_135",nameB="opls_135"} 64: type[141]={name="opls_140",nameB="opls_140"} 64: type[142]={name="opls_140",nameB="opls_140"} 64: type[143]={name="opls_140",nameB="opls_140"} 64: type[144]={name="opls_235",nameB="opls_235"} 64: type[145]={name="opls_236",nameB="opls_236"} 64: type[146]={name="opls_238",nameB="opls_238"} 64: type[147]={name="opls_241",nameB="opls_241"} 64: type[148]={name="opls_224B",nameB="opls_224B"} 64: type[149]={name="opls_140",nameB="opls_140"} 64: type[150]={name="opls_135",nameB="opls_135"} 64: type[151]={name="opls_140",nameB="opls_140"} 64: type[152]={name="opls_140",nameB="opls_140"} 64: type[153]={name="opls_140",nameB="opls_140"} 64: type[154]={name="opls_235",nameB="opls_235"} 64: type[155]={name="opls_236",nameB="opls_236"} 64: residue (10): 64: residue[0]={name="LYS", nr=1, ic=' '} 64: residue[1]={name="VAL", nr=2, ic=' '} 64: residue[2]={name="PHE", nr=3, ic=' '} 64: residue[3]={name="GLY", nr=4, ic=' '} 64: residue[4]={name="ARG", nr=5, ic=' '} 64: residue[5]={name="CYS", nr=6, ic=' '} 64: residue[6]={name="GLU", nr=7, ic=' '} 64: residue[7]={name="LEU", nr=8, ic=' '} 64: residue[8]={name="ALA", nr=9, ic=' '} 64: residue[9]={name="ALA", nr=10, ic=' '} 64: excls: 64: numLists=156 64: numElements=1828 64: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 64: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 64: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 64: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 64: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 64: 23, 24, 25, 26} 64: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 64: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 64: 14, 15, 22, 23, 24} 64: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 64: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 64: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 64: 16, 17, 18, 22} 64: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 64: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 64: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 64: 17, 18, 19, 20, 21} 64: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 64: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 64: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 64: 20, 21} 64: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 64: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 64: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 64: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 64: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 64: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 64: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 64: 26, 27, 28, 38} 64: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 64: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 64: 30, 34, 38, 39, 40} 64: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 64: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 64: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 64: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 64: 40} 64: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 64: 34, 35, 36, 37, 38, 39, 40} 64: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 64: 36, 37, 38} 64: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 64: 36, 37, 38} 64: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 64: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 64: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 64: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 64: 36, 37, 38} 64: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 64: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 64: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 64: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 64: 40, 41, 42, 43, 44, 58} 64: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 64: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 64: 45, 46, 47, 58, 59, 60} 64: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 64: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 64: 48, 50, 58, 59, 60, 61, 62} 64: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 64: 60} 64: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 64: 50, 51, 52, 54, 58, 59, 60} 64: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 64: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 64: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 64: 52, 53, 54, 55, 56, 58} 64: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 64: 54, 56, 57} 64: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 64: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 64: 55, 56, 57} 64: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 64: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 64: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 64: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 64: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 64: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 64: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 64: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 64: 60, 61, 62, 63, 64, 65} 64: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 64: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 64: 65, 66, 67} 64: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 64: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 64: 68, 69} 64: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 64: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 64: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 64: 70, 71, 89} 64: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 64: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 64: 72, 73, 74, 89, 90, 91} 64: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 64: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 64: 75, 76, 77, 89, 90, 91, 92, 93} 64: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 64: 91} 64: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 64: 77, 78, 79, 80, 89, 90, 91} 64: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 64: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 64: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 64: 79, 80, 81, 82, 89} 64: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 64: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 64: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 64: 81, 82, 83, 86} 64: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 64: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 64: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 64: 84, 85, 86, 87, 88} 64: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 64: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 64: 87, 88} 64: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 64: excls[84][num=6]={80, 82, 83, 84, 85, 86} 64: excls[85][num=6]={80, 82, 83, 84, 85, 86} 64: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 64: excls[87][num=6]={80, 82, 83, 86, 87, 88} 64: excls[88][num=6]={80, 82, 83, 86, 87, 88} 64: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 64: 91, 92, 93, 94, 95, 100} 64: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 64: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 64: 96, 97, 98, 100, 101, 102} 64: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 64: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 64: 99, 100, 101, 102, 103, 104} 64: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 64: 102} 64: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 64: 101, 102} 64: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 64: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 64: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 64: excls[99][num=6]={93, 95, 96, 97, 98, 99} 64: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 64: 102, 103, 104, 105, 106, 115} 64: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 64: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 64: 106, 107, 108, 109, 115, 116, 117} 64: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 64: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 64: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 64: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 64: 115, 116, 117} 64: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 64: 110, 111, 112, 113, 114, 115, 116, 117} 64: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 64: 112, 115} 64: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 64: 112, 115} 64: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 64: 112, 113, 114, 115} 64: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 64: 114} 64: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 64: 114} 64: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 64: 114} 64: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 64: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 64: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 64: 115, 116, 117, 118, 119, 120, 121, 134} 64: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 64: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 64: 120, 121, 122, 123, 124, 134, 135, 136} 64: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 64: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 64: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 64: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 64: 134, 135, 136} 64: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 64: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 64: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 64: 130, 134} 64: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 64: 130, 134} 64: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 64: 127, 128, 129, 130, 131, 132, 133, 134} 64: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 64: 129, 130, 131, 132, 133} 64: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 64: 129, 130, 131, 132, 133} 64: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 64: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 64: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 64: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 64: 129, 130, 131, 132, 133} 64: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 64: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 64: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 64: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 64: 134, 135, 136, 137, 138, 139, 140, 144} 64: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 64: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 64: 139, 140, 141, 142, 143, 144, 145, 146} 64: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 64: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 64: 142, 143, 144, 145, 146, 147, 148} 64: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 64: 144, 145, 146} 64: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 64: 144, 145, 146} 64: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 64: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 64: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 64: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 64: 144, 145, 146, 147, 148, 149, 150, 154} 64: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 64: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 64: 149, 150, 151, 152, 153, 154, 155} 64: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 64: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 64: 152, 153, 154, 155} 64: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 64: 154, 155} 64: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 64: 154, 155} 64: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 64: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 64: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 64: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 64: 154, 155} 64: excls[155][num=6]={146, 148, 149, 150, 154, 155} 64: Bond: 64: nr: 468 64: iatoms: 64: 0 type=100 (BONDS) 0 1 64: 1 type=100 (BONDS) 0 2 64: 2 type=100 (BONDS) 0 3 64: 3 type=101 (BONDS) 0 4 64: 4 type=102 (BONDS) 4 5 64: 5 type=103 (BONDS) 4 6 64: 6 type=104 (BONDS) 4 22 64: 7 type=102 (BONDS) 6 7 64: 8 type=102 (BONDS) 6 8 64: 9 type=103 (BONDS) 6 9 64: 10 type=102 (BONDS) 9 10 64: 11 type=102 (BONDS) 9 11 64: 12 type=103 (BONDS) 9 12 64: 13 type=102 (BONDS) 12 13 64: 14 type=102 (BONDS) 12 14 64: 15 type=103 (BONDS) 12 15 64: 16 type=102 (BONDS) 15 16 64: 17 type=102 (BONDS) 15 17 64: 18 type=101 (BONDS) 15 18 64: 19 type=100 (BONDS) 18 19 64: 20 type=100 (BONDS) 18 20 64: 21 type=100 (BONDS) 18 21 64: 22 type=105 (BONDS) 22 23 64: 23 type=106 (BONDS) 22 24 64: 24 type=100 (BONDS) 24 25 64: 25 type=107 (BONDS) 24 26 64: 26 type=102 (BONDS) 26 27 64: 27 type=103 (BONDS) 26 28 64: 28 type=104 (BONDS) 26 38 64: 29 type=102 (BONDS) 28 29 64: 30 type=103 (BONDS) 28 30 64: 31 type=103 (BONDS) 28 34 64: 32 type=102 (BONDS) 30 31 64: 33 type=102 (BONDS) 30 32 64: 34 type=102 (BONDS) 30 33 64: 35 type=102 (BONDS) 34 35 64: 36 type=102 (BONDS) 34 36 64: 37 type=102 (BONDS) 34 37 64: 38 type=105 (BONDS) 38 39 64: 39 type=106 (BONDS) 38 40 64: 40 type=100 (BONDS) 40 41 64: 41 type=107 (BONDS) 40 42 64: 42 type=102 (BONDS) 42 43 64: 43 type=103 (BONDS) 42 44 64: 44 type=104 (BONDS) 42 58 64: 45 type=102 (BONDS) 44 45 64: 46 type=102 (BONDS) 44 46 64: 47 type=108 (BONDS) 44 47 64: 48 type=109 (BONDS) 47 48 64: 49 type=109 (BONDS) 47 50 64: 50 type=110 (BONDS) 48 49 64: 51 type=109 (BONDS) 48 52 64: 52 type=110 (BONDS) 50 51 64: 53 type=109 (BONDS) 50 54 64: 54 type=110 (BONDS) 52 53 64: 55 type=109 (BONDS) 52 56 64: 56 type=110 (BONDS) 54 55 64: 57 type=109 (BONDS) 54 56 64: 58 type=110 (BONDS) 56 57 64: 59 type=105 (BONDS) 58 59 64: 60 type=106 (BONDS) 58 60 64: 61 type=100 (BONDS) 60 61 64: 62 type=107 (BONDS) 60 62 64: 63 type=102 (BONDS) 62 63 64: 64 type=102 (BONDS) 62 64 64: 65 type=104 (BONDS) 62 65 64: 66 type=105 (BONDS) 65 66 64: 67 type=106 (BONDS) 65 67 64: 68 type=100 (BONDS) 67 68 64: 69 type=107 (BONDS) 67 69 64: 70 type=102 (BONDS) 69 70 64: 71 type=103 (BONDS) 69 71 64: 72 type=104 (BONDS) 69 89 64: 73 type=102 (BONDS) 71 72 64: 74 type=102 (BONDS) 71 73 64: 75 type=103 (BONDS) 71 74 64: 76 type=102 (BONDS) 74 75 64: 77 type=102 (BONDS) 74 76 64: 78 type=103 (BONDS) 74 77 64: 79 type=102 (BONDS) 77 78 64: 80 type=102 (BONDS) 77 79 64: 81 type=111 (BONDS) 77 80 64: 82 type=100 (BONDS) 80 81 64: 83 type=112 (BONDS) 80 82 64: 84 type=112 (BONDS) 82 83 64: 85 type=112 (BONDS) 82 86 64: 86 type=100 (BONDS) 83 84 64: 87 type=100 (BONDS) 83 85 64: 88 type=100 (BONDS) 86 87 64: 89 type=100 (BONDS) 86 88 64: 90 type=105 (BONDS) 89 90 64: 91 type=106 (BONDS) 89 91 64: 92 type=100 (BONDS) 91 92 64: 93 type=107 (BONDS) 91 93 64: 94 type=102 (BONDS) 93 94 64: 95 type=103 (BONDS) 93 95 64: 96 type=104 (BONDS) 93 100 64: 97 type=102 (BONDS) 95 96 64: 98 type=102 (BONDS) 95 97 64: 99 type=113 (BONDS) 95 98 64: 100 type=114 (BONDS) 98 99 64: 101 type=105 (BONDS) 100 101 64: 102 type=106 (BONDS) 100 102 64: 103 type=100 (BONDS) 102 103 64: 104 type=107 (BONDS) 102 104 64: 105 type=102 (BONDS) 104 105 64: 106 type=103 (BONDS) 104 106 64: 107 type=104 (BONDS) 104 115 64: 108 type=102 (BONDS) 106 107 64: 109 type=102 (BONDS) 106 108 64: 110 type=103 (BONDS) 106 109 64: 111 type=102 (BONDS) 109 110 64: 112 type=102 (BONDS) 109 111 64: 113 type=104 (BONDS) 109 112 64: 114 type=115 (BONDS) 112 113 64: 115 type=115 (BONDS) 112 114 64: 116 type=105 (BONDS) 115 116 64: 117 type=106 (BONDS) 115 117 64: 118 type=100 (BONDS) 117 118 64: 119 type=107 (BONDS) 117 119 64: 120 type=102 (BONDS) 119 120 64: 121 type=103 (BONDS) 119 121 64: 122 type=104 (BONDS) 119 134 64: 123 type=102 (BONDS) 121 122 64: 124 type=102 (BONDS) 121 123 64: 125 type=103 (BONDS) 121 124 64: 126 type=102 (BONDS) 124 125 64: 127 type=103 (BONDS) 124 126 64: 128 type=103 (BONDS) 124 130 64: 129 type=102 (BONDS) 126 127 64: 130 type=102 (BONDS) 126 128 64: 131 type=102 (BONDS) 126 129 64: 132 type=102 (BONDS) 130 131 64: 133 type=102 (BONDS) 130 132 64: 134 type=102 (BONDS) 130 133 64: 135 type=105 (BONDS) 134 135 64: 136 type=106 (BONDS) 134 136 64: 137 type=100 (BONDS) 136 137 64: 138 type=107 (BONDS) 136 138 64: 139 type=102 (BONDS) 138 139 64: 140 type=103 (BONDS) 138 140 64: 141 type=104 (BONDS) 138 144 64: 142 type=102 (BONDS) 140 141 64: 143 type=102 (BONDS) 140 142 64: 144 type=102 (BONDS) 140 143 64: 145 type=105 (BONDS) 144 145 64: 146 type=106 (BONDS) 144 146 64: 147 type=100 (BONDS) 146 147 64: 148 type=107 (BONDS) 146 148 64: 149 type=102 (BONDS) 148 149 64: 150 type=103 (BONDS) 148 150 64: 151 type=104 (BONDS) 148 154 64: 152 type=102 (BONDS) 150 151 64: 153 type=102 (BONDS) 150 152 64: 154 type=102 (BONDS) 150 153 64: 155 type=105 (BONDS) 154 155 64: G96Bond: 64: nr: 0 64: Morse: 64: nr: 0 64: Cubic Bonds: 64: nr: 0 64: Connect Bonds: 64: nr: 0 64: Harmonic Pot.: 64: nr: 0 64: FENE Bonds: 64: nr: 0 64: Tab. Bonds: 64: nr: 0 64: Tab. Bonds NC: 64: nr: 0 64: Restraint Pot.: 64: nr: 0 64: Angle: 64: nr: 1124 64: iatoms: 64: 0 type=116 (ANGLES) 1 0 2 64: 1 type=116 (ANGLES) 1 0 3 64: 2 type=116 (ANGLES) 1 0 4 64: 3 type=116 (ANGLES) 2 0 3 64: 4 type=116 (ANGLES) 2 0 4 64: 5 type=116 (ANGLES) 3 0 4 64: 6 type=116 (ANGLES) 0 4 5 64: 7 type=117 (ANGLES) 0 4 6 64: 8 type=117 (ANGLES) 0 4 22 64: 9 type=118 (ANGLES) 5 4 6 64: 10 type=116 (ANGLES) 5 4 22 64: 11 type=119 (ANGLES) 6 4 22 64: 12 type=118 (ANGLES) 4 6 7 64: 13 type=118 (ANGLES) 4 6 8 64: 14 type=120 (ANGLES) 4 6 9 64: 15 type=121 (ANGLES) 7 6 8 64: 16 type=118 (ANGLES) 7 6 9 64: 17 type=118 (ANGLES) 8 6 9 64: 18 type=118 (ANGLES) 6 9 10 64: 19 type=118 (ANGLES) 6 9 11 64: 20 type=120 (ANGLES) 6 9 12 64: 21 type=121 (ANGLES) 10 9 11 64: 22 type=118 (ANGLES) 10 9 12 64: 23 type=118 (ANGLES) 11 9 12 64: 24 type=118 (ANGLES) 9 12 13 64: 25 type=118 (ANGLES) 9 12 14 64: 26 type=120 (ANGLES) 9 12 15 64: 27 type=121 (ANGLES) 13 12 14 64: 28 type=118 (ANGLES) 13 12 15 64: 29 type=118 (ANGLES) 14 12 15 64: 30 type=118 (ANGLES) 12 15 16 64: 31 type=118 (ANGLES) 12 15 17 64: 32 type=117 (ANGLES) 12 15 18 64: 33 type=121 (ANGLES) 16 15 17 64: 34 type=116 (ANGLES) 16 15 18 64: 35 type=116 (ANGLES) 17 15 18 64: 36 type=116 (ANGLES) 15 18 19 64: 37 type=116 (ANGLES) 15 18 20 64: 38 type=116 (ANGLES) 15 18 21 64: 39 type=116 (ANGLES) 19 18 20 64: 40 type=116 (ANGLES) 19 18 21 64: 41 type=116 (ANGLES) 20 18 21 64: 42 type=122 (ANGLES) 4 22 23 64: 43 type=123 (ANGLES) 4 22 24 64: 44 type=124 (ANGLES) 23 22 24 64: 45 type=125 (ANGLES) 22 24 25 64: 46 type=126 (ANGLES) 22 24 26 64: 47 type=127 (ANGLES) 25 24 26 64: 48 type=116 (ANGLES) 24 26 27 64: 49 type=128 (ANGLES) 24 26 28 64: 50 type=129 (ANGLES) 24 26 38 64: 51 type=118 (ANGLES) 27 26 28 64: 52 type=116 (ANGLES) 27 26 38 64: 53 type=119 (ANGLES) 28 26 38 64: 54 type=118 (ANGLES) 26 28 29 64: 55 type=120 (ANGLES) 26 28 30 64: 56 type=120 (ANGLES) 26 28 34 64: 57 type=118 (ANGLES) 29 28 30 64: 58 type=118 (ANGLES) 29 28 34 64: 59 type=120 (ANGLES) 30 28 34 64: 60 type=118 (ANGLES) 28 30 31 64: 61 type=118 (ANGLES) 28 30 32 64: 62 type=118 (ANGLES) 28 30 33 64: 63 type=121 (ANGLES) 31 30 32 64: 64 type=121 (ANGLES) 31 30 33 64: 65 type=121 (ANGLES) 32 30 33 64: 66 type=118 (ANGLES) 28 34 35 64: 67 type=118 (ANGLES) 28 34 36 64: 68 type=118 (ANGLES) 28 34 37 64: 69 type=121 (ANGLES) 35 34 36 64: 70 type=121 (ANGLES) 35 34 37 64: 71 type=121 (ANGLES) 36 34 37 64: 72 type=122 (ANGLES) 26 38 39 64: 73 type=123 (ANGLES) 26 38 40 64: 74 type=124 (ANGLES) 39 38 40 64: 75 type=125 (ANGLES) 38 40 41 64: 76 type=126 (ANGLES) 38 40 42 64: 77 type=127 (ANGLES) 41 40 42 64: 78 type=116 (ANGLES) 40 42 43 64: 79 type=128 (ANGLES) 40 42 44 64: 80 type=129 (ANGLES) 40 42 58 64: 81 type=118 (ANGLES) 43 42 44 64: 82 type=116 (ANGLES) 43 42 58 64: 83 type=119 (ANGLES) 44 42 58 64: 84 type=118 (ANGLES) 42 44 45 64: 85 type=118 (ANGLES) 42 44 46 64: 86 type=130 (ANGLES) 42 44 47 64: 87 type=121 (ANGLES) 45 44 46 64: 88 type=116 (ANGLES) 45 44 47 64: 89 type=116 (ANGLES) 46 44 47 64: 90 type=131 (ANGLES) 44 47 48 64: 91 type=131 (ANGLES) 44 47 50 64: 92 type=132 (ANGLES) 48 47 50 64: 93 type=133 (ANGLES) 47 48 49 64: 94 type=132 (ANGLES) 47 48 52 64: 95 type=133 (ANGLES) 49 48 52 64: 96 type=133 (ANGLES) 47 50 51 64: 97 type=132 (ANGLES) 47 50 54 64: 98 type=133 (ANGLES) 51 50 54 64: 99 type=133 (ANGLES) 48 52 53 64: 100 type=132 (ANGLES) 48 52 56 64: 101 type=133 (ANGLES) 53 52 56 64: 102 type=133 (ANGLES) 50 54 55 64: 103 type=132 (ANGLES) 50 54 56 64: 104 type=133 (ANGLES) 55 54 56 64: 105 type=132 (ANGLES) 52 56 54 64: 106 type=133 (ANGLES) 52 56 57 64: 107 type=133 (ANGLES) 54 56 57 64: 108 type=122 (ANGLES) 42 58 59 64: 109 type=123 (ANGLES) 42 58 60 64: 110 type=124 (ANGLES) 59 58 60 64: 111 type=125 (ANGLES) 58 60 61 64: 112 type=126 (ANGLES) 58 60 62 64: 113 type=127 (ANGLES) 61 60 62 64: 114 type=116 (ANGLES) 60 62 63 64: 115 type=116 (ANGLES) 60 62 64 64: 116 type=129 (ANGLES) 60 62 65 64: 117 type=121 (ANGLES) 63 62 64 64: 118 type=116 (ANGLES) 63 62 65 64: 119 type=116 (ANGLES) 64 62 65 64: 120 type=122 (ANGLES) 62 65 66 64: 121 type=123 (ANGLES) 62 65 67 64: 122 type=124 (ANGLES) 66 65 67 64: 123 type=125 (ANGLES) 65 67 68 64: 124 type=126 (ANGLES) 65 67 69 64: 125 type=127 (ANGLES) 68 67 69 64: 126 type=116 (ANGLES) 67 69 70 64: 127 type=128 (ANGLES) 67 69 71 64: 128 type=129 (ANGLES) 67 69 89 64: 129 type=118 (ANGLES) 70 69 71 64: 130 type=116 (ANGLES) 70 69 89 64: 131 type=119 (ANGLES) 71 69 89 64: 132 type=118 (ANGLES) 69 71 72 64: 133 type=118 (ANGLES) 69 71 73 64: 134 type=120 (ANGLES) 69 71 74 64: 135 type=121 (ANGLES) 72 71 73 64: 136 type=118 (ANGLES) 72 71 74 64: 137 type=118 (ANGLES) 73 71 74 64: 138 type=118 (ANGLES) 71 74 75 64: 139 type=118 (ANGLES) 71 74 76 64: 140 type=120 (ANGLES) 71 74 77 64: 141 type=121 (ANGLES) 75 74 76 64: 142 type=118 (ANGLES) 75 74 77 64: 143 type=118 (ANGLES) 76 74 77 64: 144 type=118 (ANGLES) 74 77 78 64: 145 type=118 (ANGLES) 74 77 79 64: 146 type=117 (ANGLES) 74 77 80 64: 147 type=121 (ANGLES) 78 77 79 64: 148 type=116 (ANGLES) 78 77 80 64: 149 type=116 (ANGLES) 79 77 80 64: 150 type=134 (ANGLES) 77 80 81 64: 151 type=135 (ANGLES) 77 80 82 64: 152 type=133 (ANGLES) 81 80 82 64: 153 type=131 (ANGLES) 80 82 83 64: 154 type=131 (ANGLES) 80 82 86 64: 155 type=131 (ANGLES) 83 82 86 64: 156 type=133 (ANGLES) 82 83 84 64: 157 type=133 (ANGLES) 82 83 85 64: 158 type=133 (ANGLES) 84 83 85 64: 159 type=133 (ANGLES) 82 86 87 64: 160 type=133 (ANGLES) 82 86 88 64: 161 type=133 (ANGLES) 87 86 88 64: 162 type=122 (ANGLES) 69 89 90 64: 163 type=123 (ANGLES) 69 89 91 64: 164 type=124 (ANGLES) 90 89 91 64: 165 type=125 (ANGLES) 89 91 92 64: 166 type=126 (ANGLES) 89 91 93 64: 167 type=127 (ANGLES) 92 91 93 64: 168 type=116 (ANGLES) 91 93 94 64: 169 type=128 (ANGLES) 91 93 95 64: 170 type=129 (ANGLES) 91 93 100 64: 171 type=118 (ANGLES) 94 93 95 64: 172 type=116 (ANGLES) 94 93 100 64: 173 type=119 (ANGLES) 95 93 100 64: 174 type=118 (ANGLES) 93 95 96 64: 175 type=118 (ANGLES) 93 95 97 64: 176 type=136 (ANGLES) 93 95 98 64: 177 type=121 (ANGLES) 96 95 97 64: 178 type=116 (ANGLES) 96 95 98 64: 179 type=116 (ANGLES) 97 95 98 64: 180 type=137 (ANGLES) 95 98 99 64: 181 type=122 (ANGLES) 93 100 101 64: 182 type=123 (ANGLES) 93 100 102 64: 183 type=124 (ANGLES) 101 100 102 64: 184 type=125 (ANGLES) 100 102 103 64: 185 type=126 (ANGLES) 100 102 104 64: 186 type=127 (ANGLES) 103 102 104 64: 187 type=116 (ANGLES) 102 104 105 64: 188 type=128 (ANGLES) 102 104 106 64: 189 type=129 (ANGLES) 102 104 115 64: 190 type=118 (ANGLES) 105 104 106 64: 191 type=116 (ANGLES) 105 104 115 64: 192 type=119 (ANGLES) 106 104 115 64: 193 type=118 (ANGLES) 104 106 107 64: 194 type=118 (ANGLES) 104 106 108 64: 195 type=120 (ANGLES) 104 106 109 64: 196 type=121 (ANGLES) 107 106 108 64: 197 type=118 (ANGLES) 107 106 109 64: 198 type=118 (ANGLES) 108 106 109 64: 199 type=118 (ANGLES) 106 109 110 64: 200 type=118 (ANGLES) 106 109 111 64: 201 type=119 (ANGLES) 106 109 112 64: 202 type=121 (ANGLES) 110 109 111 64: 203 type=116 (ANGLES) 110 109 112 64: 204 type=116 (ANGLES) 111 109 112 64: 205 type=138 (ANGLES) 109 112 113 64: 206 type=138 (ANGLES) 109 112 114 64: 207 type=139 (ANGLES) 113 112 114 64: 208 type=122 (ANGLES) 104 115 116 64: 209 type=123 (ANGLES) 104 115 117 64: 210 type=124 (ANGLES) 116 115 117 64: 211 type=125 (ANGLES) 115 117 118 64: 212 type=126 (ANGLES) 115 117 119 64: 213 type=127 (ANGLES) 118 117 119 64: 214 type=116 (ANGLES) 117 119 120 64: 215 type=128 (ANGLES) 117 119 121 64: 216 type=129 (ANGLES) 117 119 134 64: 217 type=118 (ANGLES) 120 119 121 64: 218 type=116 (ANGLES) 120 119 134 64: 219 type=119 (ANGLES) 121 119 134 64: 220 type=118 (ANGLES) 119 121 122 64: 221 type=118 (ANGLES) 119 121 123 64: 222 type=120 (ANGLES) 119 121 124 64: 223 type=121 (ANGLES) 122 121 123 64: 224 type=118 (ANGLES) 122 121 124 64: 225 type=118 (ANGLES) 123 121 124 64: 226 type=118 (ANGLES) 121 124 125 64: 227 type=120 (ANGLES) 121 124 126 64: 228 type=120 (ANGLES) 121 124 130 64: 229 type=118 (ANGLES) 125 124 126 64: 230 type=118 (ANGLES) 125 124 130 64: 231 type=120 (ANGLES) 126 124 130 64: 232 type=118 (ANGLES) 124 126 127 64: 233 type=118 (ANGLES) 124 126 128 64: 234 type=118 (ANGLES) 124 126 129 64: 235 type=121 (ANGLES) 127 126 128 64: 236 type=121 (ANGLES) 127 126 129 64: 237 type=121 (ANGLES) 128 126 129 64: 238 type=118 (ANGLES) 124 130 131 64: 239 type=118 (ANGLES) 124 130 132 64: 240 type=118 (ANGLES) 124 130 133 64: 241 type=121 (ANGLES) 131 130 132 64: 242 type=121 (ANGLES) 131 130 133 64: 243 type=121 (ANGLES) 132 130 133 64: 244 type=122 (ANGLES) 119 134 135 64: 245 type=123 (ANGLES) 119 134 136 64: 246 type=124 (ANGLES) 135 134 136 64: 247 type=125 (ANGLES) 134 136 137 64: 248 type=126 (ANGLES) 134 136 138 64: 249 type=127 (ANGLES) 137 136 138 64: 250 type=116 (ANGLES) 136 138 139 64: 251 type=128 (ANGLES) 136 138 140 64: 252 type=129 (ANGLES) 136 138 144 64: 253 type=118 (ANGLES) 139 138 140 64: 254 type=116 (ANGLES) 139 138 144 64: 255 type=119 (ANGLES) 140 138 144 64: 256 type=118 (ANGLES) 138 140 141 64: 257 type=118 (ANGLES) 138 140 142 64: 258 type=118 (ANGLES) 138 140 143 64: 259 type=121 (ANGLES) 141 140 142 64: 260 type=121 (ANGLES) 141 140 143 64: 261 type=121 (ANGLES) 142 140 143 64: 262 type=122 (ANGLES) 138 144 145 64: 263 type=123 (ANGLES) 138 144 146 64: 264 type=124 (ANGLES) 145 144 146 64: 265 type=125 (ANGLES) 144 146 147 64: 266 type=126 (ANGLES) 144 146 148 64: 267 type=127 (ANGLES) 147 146 148 64: 268 type=116 (ANGLES) 146 148 149 64: 269 type=128 (ANGLES) 146 148 150 64: 270 type=129 (ANGLES) 146 148 154 64: 271 type=118 (ANGLES) 149 148 150 64: 272 type=116 (ANGLES) 149 148 154 64: 273 type=119 (ANGLES) 150 148 154 64: 274 type=118 (ANGLES) 148 150 151 64: 275 type=118 (ANGLES) 148 150 152 64: 276 type=118 (ANGLES) 148 150 153 64: 277 type=121 (ANGLES) 151 150 152 64: 278 type=121 (ANGLES) 151 150 153 64: 279 type=121 (ANGLES) 152 150 153 64: 280 type=122 (ANGLES) 148 154 155 64: G96Angle: 64: nr: 0 64: Restr. Angles: 64: nr: 0 64: Lin. Angle: 64: nr: 0 64: Bond-Cross: 64: nr: 0 64: BA-Cross: 64: nr: 0 64: U-B: 64: nr: 0 64: Quartic Angles: 64: nr: 0 64: Tab. Angles: 64: nr: 0 64: Proper Dih.: 64: nr: 145 64: iatoms: 64: 0 type=140 (PDIHS) 4 24 22 23 64: 1 type=141 (PDIHS) 22 26 24 25 64: 2 type=140 (PDIHS) 26 40 38 39 64: 3 type=141 (PDIHS) 38 42 40 41 64: 4 type=140 (PDIHS) 42 60 58 59 64: 5 type=142 (PDIHS) 44 47 50 48 64: 6 type=142 (PDIHS) 47 52 48 49 64: 7 type=142 (PDIHS) 47 54 50 51 64: 8 type=142 (PDIHS) 48 56 52 53 64: 9 type=142 (PDIHS) 50 56 54 55 64: 10 type=142 (PDIHS) 52 54 56 57 64: 11 type=141 (PDIHS) 58 62 60 61 64: 12 type=140 (PDIHS) 62 67 65 66 64: 13 type=141 (PDIHS) 65 69 67 68 64: 14 type=140 (PDIHS) 69 91 89 90 64: 15 type=141 (PDIHS) 77 82 80 81 64: 16 type=140 (PDIHS) 80 83 82 86 64: 17 type=141 (PDIHS) 82 84 83 85 64: 18 type=141 (PDIHS) 82 87 86 88 64: 19 type=141 (PDIHS) 89 93 91 92 64: 20 type=140 (PDIHS) 93 102 100 101 64: 21 type=141 (PDIHS) 100 104 102 103 64: 22 type=140 (PDIHS) 104 117 115 116 64: 23 type=140 (PDIHS) 109 113 112 114 64: 24 type=141 (PDIHS) 115 119 117 118 64: 25 type=140 (PDIHS) 119 136 134 135 64: 26 type=141 (PDIHS) 134 138 136 137 64: 27 type=140 (PDIHS) 138 146 144 145 64: 28 type=141 (PDIHS) 144 148 146 147 64: Ryckaert-Bell.: 64: nr: 1565 64: iatoms: 64: 0 type=143 (RBDIHS) 1 0 4 5 64: 1 type=144 (RBDIHS) 1 0 4 6 64: 2 type=144 (RBDIHS) 1 0 4 22 64: 3 type=143 (RBDIHS) 2 0 4 5 64: 4 type=144 (RBDIHS) 2 0 4 6 64: 5 type=144 (RBDIHS) 2 0 4 22 64: 6 type=143 (RBDIHS) 3 0 4 5 64: 7 type=144 (RBDIHS) 3 0 4 6 64: 8 type=144 (RBDIHS) 3 0 4 22 64: 9 type=145 (RBDIHS) 0 4 6 9 64: 10 type=146 (RBDIHS) 22 4 6 9 64: 11 type=147 (RBDIHS) 0 4 6 7 64: 12 type=147 (RBDIHS) 0 4 6 8 64: 13 type=148 (RBDIHS) 5 4 6 7 64: 14 type=148 (RBDIHS) 5 4 6 8 64: 15 type=148 (RBDIHS) 5 4 6 9 64: 16 type=149 (RBDIHS) 22 4 6 7 64: 17 type=149 (RBDIHS) 22 4 6 8 64: 18 type=150 (RBDIHS) 0 4 22 24 64: 19 type=151 (RBDIHS) 6 4 22 24 64: 20 type=148 (RBDIHS) 4 6 9 10 64: 21 type=148 (RBDIHS) 4 6 9 11 64: 22 type=152 (RBDIHS) 4 6 9 12 64: 23 type=148 (RBDIHS) 7 6 9 10 64: 24 type=148 (RBDIHS) 7 6 9 11 64: 25 type=148 (RBDIHS) 7 6 9 12 64: 26 type=148 (RBDIHS) 8 6 9 10 64: 27 type=148 (RBDIHS) 8 6 9 11 64: 28 type=148 (RBDIHS) 8 6 9 12 64: 29 type=148 (RBDIHS) 6 9 12 13 64: 30 type=148 (RBDIHS) 6 9 12 14 64: 31 type=152 (RBDIHS) 6 9 12 15 64: 32 type=148 (RBDIHS) 10 9 12 13 64: 33 type=148 (RBDIHS) 10 9 12 14 64: 34 type=148 (RBDIHS) 10 9 12 15 64: 35 type=148 (RBDIHS) 11 9 12 13 64: 36 type=148 (RBDIHS) 11 9 12 14 64: 37 type=148 (RBDIHS) 11 9 12 15 64: 38 type=148 (RBDIHS) 9 12 15 16 64: 39 type=148 (RBDIHS) 9 12 15 17 64: 40 type=153 (RBDIHS) 9 12 15 18 64: 41 type=148 (RBDIHS) 13 12 15 16 64: 42 type=148 (RBDIHS) 13 12 15 17 64: 43 type=154 (RBDIHS) 13 12 15 18 64: 44 type=148 (RBDIHS) 14 12 15 16 64: 45 type=148 (RBDIHS) 14 12 15 17 64: 46 type=154 (RBDIHS) 14 12 15 18 64: 47 type=144 (RBDIHS) 12 15 18 19 64: 48 type=144 (RBDIHS) 12 15 18 20 64: 49 type=144 (RBDIHS) 12 15 18 21 64: 50 type=143 (RBDIHS) 16 15 18 19 64: 51 type=143 (RBDIHS) 16 15 18 20 64: 52 type=143 (RBDIHS) 16 15 18 21 64: 53 type=143 (RBDIHS) 17 15 18 19 64: 54 type=143 (RBDIHS) 17 15 18 20 64: 55 type=143 (RBDIHS) 17 15 18 21 64: 56 type=155 (RBDIHS) 4 22 24 25 64: 57 type=156 (RBDIHS) 4 22 24 26 64: 58 type=155 (RBDIHS) 23 22 24 25 64: 59 type=157 (RBDIHS) 23 22 24 26 64: 60 type=158 (RBDIHS) 22 24 26 28 64: 61 type=159 (RBDIHS) 22 24 26 38 64: 62 type=160 (RBDIHS) 24 26 28 30 64: 63 type=160 (RBDIHS) 24 26 28 34 64: 64 type=161 (RBDIHS) 38 26 28 30 64: 65 type=161 (RBDIHS) 38 26 28 34 64: 66 type=147 (RBDIHS) 24 26 28 29 64: 67 type=148 (RBDIHS) 27 26 28 29 64: 68 type=148 (RBDIHS) 27 26 28 30 64: 69 type=148 (RBDIHS) 27 26 28 34 64: 70 type=149 (RBDIHS) 38 26 28 29 64: 71 type=150 (RBDIHS) 24 26 38 40 64: 72 type=151 (RBDIHS) 28 26 38 40 64: 73 type=148 (RBDIHS) 26 28 30 31 64: 74 type=148 (RBDIHS) 26 28 30 32 64: 75 type=148 (RBDIHS) 26 28 30 33 64: 76 type=148 (RBDIHS) 29 28 30 31 64: 77 type=148 (RBDIHS) 29 28 30 32 64: 78 type=148 (RBDIHS) 29 28 30 33 64: 79 type=148 (RBDIHS) 34 28 30 31 64: 80 type=148 (RBDIHS) 34 28 30 32 64: 81 type=148 (RBDIHS) 34 28 30 33 64: 82 type=148 (RBDIHS) 26 28 34 35 64: 83 type=148 (RBDIHS) 26 28 34 36 64: 84 type=148 (RBDIHS) 26 28 34 37 64: 85 type=148 (RBDIHS) 29 28 34 35 64: 86 type=148 (RBDIHS) 29 28 34 36 64: 87 type=148 (RBDIHS) 29 28 34 37 64: 88 type=148 (RBDIHS) 30 28 34 35 64: 89 type=148 (RBDIHS) 30 28 34 36 64: 90 type=148 (RBDIHS) 30 28 34 37 64: 91 type=155 (RBDIHS) 26 38 40 41 64: 92 type=156 (RBDIHS) 26 38 40 42 64: 93 type=155 (RBDIHS) 39 38 40 41 64: 94 type=157 (RBDIHS) 39 38 40 42 64: 95 type=158 (RBDIHS) 38 40 42 44 64: 96 type=159 (RBDIHS) 38 40 42 58 64: 97 type=147 (RBDIHS) 40 42 44 45 64: 98 type=147 (RBDIHS) 40 42 44 46 64: 99 type=162 (RBDIHS) 40 42 44 47 64: 100 type=148 (RBDIHS) 43 42 44 45 64: 101 type=148 (RBDIHS) 43 42 44 46 64: 102 type=163 (RBDIHS) 43 42 44 47 64: 103 type=149 (RBDIHS) 58 42 44 45 64: 104 type=149 (RBDIHS) 58 42 44 46 64: 105 type=164 (RBDIHS) 58 42 44 47 64: 106 type=150 (RBDIHS) 40 42 58 60 64: 107 type=151 (RBDIHS) 44 42 58 60 64: 108 type=165 (RBDIHS) 44 47 48 49 64: 109 type=165 (RBDIHS) 44 47 48 52 64: 110 type=165 (RBDIHS) 50 47 48 49 64: 111 type=165 (RBDIHS) 50 47 48 52 64: 112 type=165 (RBDIHS) 44 47 50 51 64: 113 type=165 (RBDIHS) 44 47 50 54 64: 114 type=165 (RBDIHS) 48 47 50 51 64: 115 type=165 (RBDIHS) 48 47 50 54 64: 116 type=165 (RBDIHS) 47 48 52 53 64: 117 type=165 (RBDIHS) 47 48 52 56 64: 118 type=165 (RBDIHS) 49 48 52 53 64: 119 type=165 (RBDIHS) 49 48 52 56 64: 120 type=165 (RBDIHS) 47 50 54 55 64: 121 type=165 (RBDIHS) 47 50 54 56 64: 122 type=165 (RBDIHS) 51 50 54 55 64: 123 type=165 (RBDIHS) 51 50 54 56 64: 124 type=165 (RBDIHS) 48 52 56 54 64: 125 type=165 (RBDIHS) 48 52 56 57 64: 126 type=165 (RBDIHS) 53 52 56 54 64: 127 type=165 (RBDIHS) 53 52 56 57 64: 128 type=165 (RBDIHS) 50 54 56 52 64: 129 type=165 (RBDIHS) 50 54 56 57 64: 130 type=165 (RBDIHS) 55 54 56 52 64: 131 type=165 (RBDIHS) 55 54 56 57 64: 132 type=155 (RBDIHS) 42 58 60 61 64: 133 type=156 (RBDIHS) 42 58 60 62 64: 134 type=155 (RBDIHS) 59 58 60 61 64: 135 type=157 (RBDIHS) 59 58 60 62 64: 136 type=159 (RBDIHS) 58 60 62 65 64: 137 type=150 (RBDIHS) 60 62 65 67 64: 138 type=155 (RBDIHS) 62 65 67 68 64: 139 type=156 (RBDIHS) 62 65 67 69 64: 140 type=155 (RBDIHS) 66 65 67 68 64: 141 type=157 (RBDIHS) 66 65 67 69 64: 142 type=158 (RBDIHS) 65 67 69 71 64: 143 type=159 (RBDIHS) 65 67 69 89 64: 144 type=166 (RBDIHS) 67 69 71 74 64: 145 type=167 (RBDIHS) 89 69 71 74 64: 146 type=147 (RBDIHS) 67 69 71 72 64: 147 type=147 (RBDIHS) 67 69 71 73 64: 148 type=148 (RBDIHS) 70 69 71 72 64: 149 type=148 (RBDIHS) 70 69 71 73 64: 150 type=148 (RBDIHS) 70 69 71 74 64: 151 type=149 (RBDIHS) 89 69 71 72 64: 152 type=149 (RBDIHS) 89 69 71 73 64: 153 type=150 (RBDIHS) 67 69 89 91 64: 154 type=151 (RBDIHS) 71 69 89 91 64: 155 type=148 (RBDIHS) 69 71 74 75 64: 156 type=148 (RBDIHS) 69 71 74 76 64: 157 type=152 (RBDIHS) 69 71 74 77 64: 158 type=148 (RBDIHS) 72 71 74 75 64: 159 type=148 (RBDIHS) 72 71 74 76 64: 160 type=148 (RBDIHS) 72 71 74 77 64: 161 type=148 (RBDIHS) 73 71 74 75 64: 162 type=148 (RBDIHS) 73 71 74 76 64: 163 type=148 (RBDIHS) 73 71 74 77 64: 164 type=148 (RBDIHS) 71 74 77 78 64: 165 type=148 (RBDIHS) 71 74 77 79 64: 166 type=153 (RBDIHS) 71 74 77 80 64: 167 type=148 (RBDIHS) 75 74 77 78 64: 168 type=148 (RBDIHS) 75 74 77 79 64: 169 type=168 (RBDIHS) 75 74 77 80 64: 170 type=148 (RBDIHS) 76 74 77 78 64: 171 type=148 (RBDIHS) 76 74 77 79 64: 172 type=168 (RBDIHS) 76 74 77 80 64: 173 type=169 (RBDIHS) 74 77 80 81 64: 174 type=170 (RBDIHS) 74 77 80 82 64: 175 type=171 (RBDIHS) 78 77 80 82 64: 176 type=171 (RBDIHS) 79 77 80 82 64: 177 type=172 (RBDIHS) 77 80 82 83 64: 178 type=172 (RBDIHS) 77 80 82 86 64: 179 type=173 (RBDIHS) 81 80 82 83 64: 180 type=173 (RBDIHS) 81 80 82 86 64: 181 type=173 (RBDIHS) 80 82 83 84 64: 182 type=173 (RBDIHS) 80 82 83 85 64: 183 type=173 (RBDIHS) 86 82 83 84 64: 184 type=173 (RBDIHS) 86 82 83 85 64: 185 type=173 (RBDIHS) 80 82 86 87 64: 186 type=173 (RBDIHS) 80 82 86 88 64: 187 type=173 (RBDIHS) 83 82 86 87 64: 188 type=173 (RBDIHS) 83 82 86 88 64: 189 type=155 (RBDIHS) 69 89 91 92 64: 190 type=156 (RBDIHS) 69 89 91 93 64: 191 type=155 (RBDIHS) 90 89 91 92 64: 192 type=157 (RBDIHS) 90 89 91 93 64: 193 type=158 (RBDIHS) 89 91 93 95 64: 194 type=159 (RBDIHS) 89 91 93 100 64: 195 type=174 (RBDIHS) 91 93 95 98 64: 196 type=175 (RBDIHS) 100 93 95 98 64: 197 type=147 (RBDIHS) 91 93 95 96 64: 198 type=147 (RBDIHS) 91 93 95 97 64: 199 type=148 (RBDIHS) 94 93 95 96 64: 200 type=148 (RBDIHS) 94 93 95 97 64: 201 type=176 (RBDIHS) 94 93 95 98 64: 202 type=149 (RBDIHS) 100 93 95 96 64: 203 type=149 (RBDIHS) 100 93 95 97 64: 204 type=150 (RBDIHS) 91 93 100 102 64: 205 type=151 (RBDIHS) 95 93 100 102 64: 206 type=177 (RBDIHS) 93 95 98 99 64: 207 type=178 (RBDIHS) 96 95 98 99 64: 208 type=178 (RBDIHS) 97 95 98 99 64: 209 type=155 (RBDIHS) 93 100 102 103 64: 210 type=156 (RBDIHS) 93 100 102 104 64: 211 type=155 (RBDIHS) 101 100 102 103 64: 212 type=157 (RBDIHS) 101 100 102 104 64: 213 type=158 (RBDIHS) 100 102 104 106 64: 214 type=159 (RBDIHS) 100 102 104 115 64: 215 type=179 (RBDIHS) 102 104 106 109 64: 216 type=180 (RBDIHS) 115 104 106 109 64: 217 type=147 (RBDIHS) 102 104 106 107 64: 218 type=147 (RBDIHS) 102 104 106 108 64: 219 type=148 (RBDIHS) 105 104 106 107 64: 220 type=148 (RBDIHS) 105 104 106 108 64: 221 type=148 (RBDIHS) 105 104 106 109 64: 222 type=149 (RBDIHS) 115 104 106 107 64: 223 type=149 (RBDIHS) 115 104 106 108 64: 224 type=150 (RBDIHS) 102 104 115 117 64: 225 type=151 (RBDIHS) 106 104 115 117 64: 226 type=148 (RBDIHS) 104 106 109 110 64: 227 type=148 (RBDIHS) 104 106 109 111 64: 228 type=181 (RBDIHS) 104 106 109 112 64: 229 type=148 (RBDIHS) 107 106 109 110 64: 230 type=148 (RBDIHS) 107 106 109 111 64: 231 type=182 (RBDIHS) 107 106 109 112 64: 232 type=148 (RBDIHS) 108 106 109 110 64: 233 type=148 (RBDIHS) 108 106 109 111 64: 234 type=182 (RBDIHS) 108 106 109 112 64: 235 type=183 (RBDIHS) 106 109 112 113 64: 236 type=183 (RBDIHS) 106 109 112 114 64: 237 type=155 (RBDIHS) 104 115 117 118 64: 238 type=156 (RBDIHS) 104 115 117 119 64: 239 type=155 (RBDIHS) 116 115 117 118 64: 240 type=157 (RBDIHS) 116 115 117 119 64: 241 type=158 (RBDIHS) 115 117 119 121 64: 242 type=159 (RBDIHS) 115 117 119 134 64: 243 type=184 (RBDIHS) 117 119 121 124 64: 244 type=185 (RBDIHS) 134 119 121 124 64: 245 type=147 (RBDIHS) 117 119 121 122 64: 246 type=147 (RBDIHS) 117 119 121 123 64: 247 type=148 (RBDIHS) 120 119 121 122 64: 248 type=148 (RBDIHS) 120 119 121 123 64: 249 type=148 (RBDIHS) 120 119 121 124 64: 250 type=149 (RBDIHS) 134 119 121 122 64: 251 type=149 (RBDIHS) 134 119 121 123 64: 252 type=150 (RBDIHS) 117 119 134 136 64: 253 type=151 (RBDIHS) 121 119 134 136 64: 254 type=148 (RBDIHS) 119 121 124 125 64: 255 type=152 (RBDIHS) 119 121 124 126 64: 256 type=152 (RBDIHS) 119 121 124 130 64: 257 type=148 (RBDIHS) 122 121 124 125 64: 258 type=148 (RBDIHS) 122 121 124 126 64: 259 type=148 (RBDIHS) 122 121 124 130 64: 260 type=148 (RBDIHS) 123 121 124 125 64: 261 type=148 (RBDIHS) 123 121 124 126 64: 262 type=148 (RBDIHS) 123 121 124 130 64: 263 type=148 (RBDIHS) 121 124 126 127 64: 264 type=148 (RBDIHS) 121 124 126 128 64: 265 type=148 (RBDIHS) 121 124 126 129 64: 266 type=148 (RBDIHS) 125 124 126 127 64: 267 type=148 (RBDIHS) 125 124 126 128 64: 268 type=148 (RBDIHS) 125 124 126 129 64: 269 type=148 (RBDIHS) 130 124 126 127 64: 270 type=148 (RBDIHS) 130 124 126 128 64: 271 type=148 (RBDIHS) 130 124 126 129 64: 272 type=148 (RBDIHS) 121 124 130 131 64: 273 type=148 (RBDIHS) 121 124 130 132 64: 274 type=148 (RBDIHS) 121 124 130 133 64: 275 type=148 (RBDIHS) 125 124 130 131 64: 276 type=148 (RBDIHS) 125 124 130 132 64: 277 type=148 (RBDIHS) 125 124 130 133 64: 278 type=148 (RBDIHS) 126 124 130 131 64: 279 type=148 (RBDIHS) 126 124 130 132 64: 280 type=148 (RBDIHS) 126 124 130 133 64: 281 type=155 (RBDIHS) 119 134 136 137 64: 282 type=156 (RBDIHS) 119 134 136 138 64: 283 type=155 (RBDIHS) 135 134 136 137 64: 284 type=157 (RBDIHS) 135 134 136 138 64: 285 type=158 (RBDIHS) 134 136 138 140 64: 286 type=159 (RBDIHS) 134 136 138 144 64: 287 type=147 (RBDIHS) 136 138 140 141 64: 288 type=147 (RBDIHS) 136 138 140 142 64: 289 type=147 (RBDIHS) 136 138 140 143 64: 290 type=148 (RBDIHS) 139 138 140 141 64: 291 type=148 (RBDIHS) 139 138 140 142 64: 292 type=148 (RBDIHS) 139 138 140 143 64: 293 type=149 (RBDIHS) 144 138 140 141 64: 294 type=149 (RBDIHS) 144 138 140 142 64: 295 type=149 (RBDIHS) 144 138 140 143 64: 296 type=150 (RBDIHS) 136 138 144 146 64: 297 type=151 (RBDIHS) 140 138 144 146 64: 298 type=155 (RBDIHS) 138 144 146 147 64: 299 type=156 (RBDIHS) 138 144 146 148 64: 300 type=155 (RBDIHS) 145 144 146 147 64: 301 type=157 (RBDIHS) 145 144 146 148 64: 302 type=158 (RBDIHS) 144 146 148 150 64: 303 type=159 (RBDIHS) 144 146 148 154 64: 304 type=147 (RBDIHS) 146 148 150 151 64: 305 type=147 (RBDIHS) 146 148 150 152 64: 306 type=147 (RBDIHS) 146 148 150 153 64: 307 type=148 (RBDIHS) 149 148 150 151 64: 308 type=148 (RBDIHS) 149 148 150 152 64: 309 type=148 (RBDIHS) 149 148 150 153 64: 310 type=149 (RBDIHS) 154 148 150 151 64: 311 type=149 (RBDIHS) 154 148 150 152 64: 312 type=149 (RBDIHS) 154 148 150 153 64: Restr. Dih.: 64: nr: 0 64: CBT Dih.: 64: nr: 0 64: Fourier Dih.: 64: nr: 0 64: Improper Dih.: 64: nr: 0 64: Per. Imp. Dih.: 64: nr: 0 64: Tab. Dih.: 64: nr: 0 64: CMAP Dih.: 64: nr: 0 64: GB 1-2 Pol.: 64: nr: 0 64: GB 1-3 Pol.: 64: nr: 0 64: GB 1-4 Pol.: 64: nr: 0 64: GB Polariz.: 64: nr: 0 64: Nonpolar Sol.: 64: nr: 0 64: LJ-14: 64: nr: 1197 64: iatoms: 64: 0 type=186 (LJ14) 0 7 64: 1 type=186 (LJ14) 0 8 64: 2 type=187 (LJ14) 0 9 64: 3 type=188 (LJ14) 0 23 64: 4 type=189 (LJ14) 0 24 64: 5 type=190 (LJ14) 1 5 64: 6 type=190 (LJ14) 1 6 64: 7 type=190 (LJ14) 1 22 64: 8 type=190 (LJ14) 2 5 64: 9 type=190 (LJ14) 2 6 64: 10 type=190 (LJ14) 2 22 64: 11 type=190 (LJ14) 3 5 64: 12 type=190 (LJ14) 3 6 64: 13 type=190 (LJ14) 3 22 64: 14 type=191 (LJ14) 4 10 64: 15 type=191 (LJ14) 4 11 64: 16 type=192 (LJ14) 4 12 64: 17 type=190 (LJ14) 4 25 64: 18 type=192 (LJ14) 4 26 64: 19 type=193 (LJ14) 5 7 64: 20 type=193 (LJ14) 5 8 64: 21 type=191 (LJ14) 5 9 64: 22 type=194 (LJ14) 5 23 64: 23 type=186 (LJ14) 5 24 64: 24 type=191 (LJ14) 6 13 64: 25 type=191 (LJ14) 6 14 64: 26 type=192 (LJ14) 6 15 64: 27 type=195 (LJ14) 6 23 64: 28 type=187 (LJ14) 6 24 64: 29 type=193 (LJ14) 7 10 64: 30 type=193 (LJ14) 7 11 64: 31 type=191 (LJ14) 7 12 64: 32 type=196 (LJ14) 7 22 64: 33 type=193 (LJ14) 8 10 64: 34 type=193 (LJ14) 8 11 64: 35 type=191 (LJ14) 8 12 64: 36 type=196 (LJ14) 8 22 64: 37 type=191 (LJ14) 9 16 64: 38 type=191 (LJ14) 9 17 64: 39 type=187 (LJ14) 9 18 64: 40 type=197 (LJ14) 9 22 64: 41 type=193 (LJ14) 10 13 64: 42 type=193 (LJ14) 10 14 64: 43 type=191 (LJ14) 10 15 64: 44 type=193 (LJ14) 11 13 64: 45 type=193 (LJ14) 11 14 64: 46 type=191 (LJ14) 11 15 64: 47 type=190 (LJ14) 12 19 64: 48 type=190 (LJ14) 12 20 64: 49 type=190 (LJ14) 12 21 64: 50 type=193 (LJ14) 13 16 64: 51 type=193 (LJ14) 13 17 64: 52 type=186 (LJ14) 13 18 64: 53 type=193 (LJ14) 14 16 64: 54 type=193 (LJ14) 14 17 64: 55 type=186 (LJ14) 14 18 64: 56 type=190 (LJ14) 16 19 64: 57 type=190 (LJ14) 16 20 64: 58 type=190 (LJ14) 16 21 64: 59 type=190 (LJ14) 17 19 64: 60 type=190 (LJ14) 17 20 64: 61 type=190 (LJ14) 17 21 64: 62 type=196 (LJ14) 22 27 64: 63 type=197 (LJ14) 22 28 64: 64 type=198 (LJ14) 22 38 64: 65 type=190 (LJ14) 23 25 64: 66 type=195 (LJ14) 23 26 64: 67 type=186 (LJ14) 24 29 64: 68 type=187 (LJ14) 24 30 64: 69 type=187 (LJ14) 24 34 64: 70 type=188 (LJ14) 24 39 64: 71 type=189 (LJ14) 24 40 64: 72 type=190 (LJ14) 25 27 64: 73 type=190 (LJ14) 25 28 64: 74 type=190 (LJ14) 25 38 64: 75 type=191 (LJ14) 26 31 64: 76 type=191 (LJ14) 26 32 64: 77 type=191 (LJ14) 26 33 64: 78 type=191 (LJ14) 26 35 64: 79 type=191 (LJ14) 26 36 64: 80 type=191 (LJ14) 26 37 64: 81 type=190 (LJ14) 26 41 64: 82 type=192 (LJ14) 26 42 64: 83 type=193 (LJ14) 27 29 64: 84 type=191 (LJ14) 27 30 64: 85 type=191 (LJ14) 27 34 64: 86 type=194 (LJ14) 27 39 64: 87 type=186 (LJ14) 27 40 64: 88 type=195 (LJ14) 28 39 64: 89 type=187 (LJ14) 28 40 64: 90 type=193 (LJ14) 29 31 64: 91 type=193 (LJ14) 29 32 64: 92 type=193 (LJ14) 29 33 64: 93 type=193 (LJ14) 29 35 64: 94 type=193 (LJ14) 29 36 64: 95 type=193 (LJ14) 29 37 64: 96 type=196 (LJ14) 29 38 64: 97 type=191 (LJ14) 30 35 64: 98 type=191 (LJ14) 30 36 64: 99 type=191 (LJ14) 30 37 64: 100 type=197 (LJ14) 30 38 64: 101 type=191 (LJ14) 31 34 64: 102 type=191 (LJ14) 32 34 64: 103 type=191 (LJ14) 33 34 64: 104 type=197 (LJ14) 34 38 64: 105 type=196 (LJ14) 38 43 64: 106 type=197 (LJ14) 38 44 64: 107 type=198 (LJ14) 38 58 64: 108 type=190 (LJ14) 39 41 64: 109 type=195 (LJ14) 39 42 64: 110 type=186 (LJ14) 40 45 64: 111 type=186 (LJ14) 40 46 64: 112 type=199 (LJ14) 40 47 64: 113 type=188 (LJ14) 40 59 64: 114 type=189 (LJ14) 40 60 64: 115 type=190 (LJ14) 41 43 64: 116 type=190 (LJ14) 41 44 64: 117 type=190 (LJ14) 41 58 64: 118 type=200 (LJ14) 42 48 64: 119 type=200 (LJ14) 42 50 64: 120 type=190 (LJ14) 42 61 64: 121 type=192 (LJ14) 42 62 64: 122 type=193 (LJ14) 43 45 64: 123 type=193 (LJ14) 43 46 64: 124 type=201 (LJ14) 43 47 64: 125 type=194 (LJ14) 43 59 64: 126 type=186 (LJ14) 43 60 64: 127 type=202 (LJ14) 44 49 64: 128 type=202 (LJ14) 44 51 64: 129 type=200 (LJ14) 44 52 64: 130 type=200 (LJ14) 44 54 64: 131 type=195 (LJ14) 44 59 64: 132 type=187 (LJ14) 44 60 64: 133 type=201 (LJ14) 45 48 64: 134 type=201 (LJ14) 45 50 64: 135 type=196 (LJ14) 45 58 64: 136 type=201 (LJ14) 46 48 64: 137 type=201 (LJ14) 46 50 64: 138 type=196 (LJ14) 46 58 64: 139 type=203 (LJ14) 47 53 64: 140 type=203 (LJ14) 47 55 64: 141 type=204 (LJ14) 47 56 64: 142 type=205 (LJ14) 47 58 64: 143 type=203 (LJ14) 48 51 64: 144 type=204 (LJ14) 48 54 64: 145 type=203 (LJ14) 48 57 64: 146 type=203 (LJ14) 49 50 64: 147 type=206 (LJ14) 49 53 64: 148 type=203 (LJ14) 49 56 64: 149 type=204 (LJ14) 50 52 64: 150 type=203 (LJ14) 50 57 64: 151 type=206 (LJ14) 51 55 64: 152 type=203 (LJ14) 51 56 64: 153 type=203 (LJ14) 52 55 64: 154 type=203 (LJ14) 53 54 64: 155 type=206 (LJ14) 53 57 64: 156 type=206 (LJ14) 55 57 64: 157 type=196 (LJ14) 58 63 64: 158 type=196 (LJ14) 58 64 64: 159 type=198 (LJ14) 58 65 64: 160 type=190 (LJ14) 59 61 64: 161 type=195 (LJ14) 59 62 64: 162 type=188 (LJ14) 60 66 64: 163 type=189 (LJ14) 60 67 64: 164 type=190 (LJ14) 61 63 64: 165 type=190 (LJ14) 61 64 64: 166 type=190 (LJ14) 61 65 64: 167 type=190 (LJ14) 62 68 64: 168 type=192 (LJ14) 62 69 64: 169 type=194 (LJ14) 63 66 64: 170 type=186 (LJ14) 63 67 64: 171 type=194 (LJ14) 64 66 64: 172 type=186 (LJ14) 64 67 64: 173 type=196 (LJ14) 65 70 64: 174 type=197 (LJ14) 65 71 64: 175 type=198 (LJ14) 65 89 64: 176 type=190 (LJ14) 66 68 64: 177 type=195 (LJ14) 66 69 64: 178 type=186 (LJ14) 67 72 64: 179 type=186 (LJ14) 67 73 64: 180 type=187 (LJ14) 67 74 64: 181 type=188 (LJ14) 67 90 64: 182 type=189 (LJ14) 67 91 64: 183 type=190 (LJ14) 68 70 64: 184 type=190 (LJ14) 68 71 64: 185 type=190 (LJ14) 68 89 64: 186 type=191 (LJ14) 69 75 64: 187 type=191 (LJ14) 69 76 64: 188 type=192 (LJ14) 69 77 64: 189 type=190 (LJ14) 69 92 64: 190 type=192 (LJ14) 69 93 64: 191 type=193 (LJ14) 70 72 64: 192 type=193 (LJ14) 70 73 64: 193 type=191 (LJ14) 70 74 64: 194 type=194 (LJ14) 70 90 64: 195 type=186 (LJ14) 70 91 64: 196 type=191 (LJ14) 71 78 64: 197 type=191 (LJ14) 71 79 64: 198 type=187 (LJ14) 71 80 64: 199 type=195 (LJ14) 71 90 64: 200 type=187 (LJ14) 71 91 64: 201 type=193 (LJ14) 72 75 64: 202 type=193 (LJ14) 72 76 64: 203 type=191 (LJ14) 72 77 64: 204 type=196 (LJ14) 72 89 64: 205 type=193 (LJ14) 73 75 64: 206 type=193 (LJ14) 73 76 64: 207 type=191 (LJ14) 73 77 64: 208 type=196 (LJ14) 73 89 64: 209 type=190 (LJ14) 74 81 64: 210 type=207 (LJ14) 74 82 64: 211 type=197 (LJ14) 74 89 64: 212 type=193 (LJ14) 75 78 64: 213 type=193 (LJ14) 75 79 64: 214 type=186 (LJ14) 75 80 64: 215 type=193 (LJ14) 76 78 64: 216 type=193 (LJ14) 76 79 64: 217 type=186 (LJ14) 76 80 64: 218 type=187 (LJ14) 77 83 64: 219 type=187 (LJ14) 77 86 64: 220 type=190 (LJ14) 78 81 64: 221 type=208 (LJ14) 78 82 64: 222 type=190 (LJ14) 79 81 64: 223 type=208 (LJ14) 79 82 64: 224 type=190 (LJ14) 80 84 64: 225 type=190 (LJ14) 80 85 64: 226 type=190 (LJ14) 80 87 64: 227 type=190 (LJ14) 80 88 64: 228 type=190 (LJ14) 81 83 64: 229 type=190 (LJ14) 81 86 64: 230 type=190 (LJ14) 83 87 64: 231 type=190 (LJ14) 83 88 64: 232 type=190 (LJ14) 84 86 64: 233 type=190 (LJ14) 85 86 64: 234 type=196 (LJ14) 89 94 64: 235 type=197 (LJ14) 89 95 64: 236 type=198 (LJ14) 89 100 64: 237 type=190 (LJ14) 90 92 64: 238 type=195 (LJ14) 90 93 64: 239 type=186 (LJ14) 91 96 64: 240 type=186 (LJ14) 91 97 64: 241 type=209 (LJ14) 91 98 64: 242 type=188 (LJ14) 91 101 64: 243 type=189 (LJ14) 91 102 64: 244 type=190 (LJ14) 92 94 64: 245 type=190 (LJ14) 92 95 64: 246 type=190 (LJ14) 92 100 64: 247 type=190 (LJ14) 93 99 64: 248 type=190 (LJ14) 93 103 64: 249 type=192 (LJ14) 93 104 64: 250 type=193 (LJ14) 94 96 64: 251 type=193 (LJ14) 94 97 64: 252 type=210 (LJ14) 94 98 64: 253 type=194 (LJ14) 94 101 64: 254 type=186 (LJ14) 94 102 64: 255 type=195 (LJ14) 95 101 64: 256 type=187 (LJ14) 95 102 64: 257 type=190 (LJ14) 96 99 64: 258 type=196 (LJ14) 96 100 64: 259 type=190 (LJ14) 97 99 64: 260 type=196 (LJ14) 97 100 64: 261 type=211 (LJ14) 98 100 64: 262 type=196 (LJ14) 100 105 64: 263 type=197 (LJ14) 100 106 64: 264 type=198 (LJ14) 100 115 64: 265 type=190 (LJ14) 101 103 64: 266 type=195 (LJ14) 101 104 64: 267 type=186 (LJ14) 102 107 64: 268 type=186 (LJ14) 102 108 64: 269 type=187 (LJ14) 102 109 64: 270 type=188 (LJ14) 102 116 64: 271 type=189 (LJ14) 102 117 64: 272 type=190 (LJ14) 103 105 64: 273 type=190 (LJ14) 103 106 64: 274 type=190 (LJ14) 103 115 64: 275 type=191 (LJ14) 104 110 64: 276 type=191 (LJ14) 104 111 64: 277 type=197 (LJ14) 104 112 64: 278 type=190 (LJ14) 104 118 64: 279 type=192 (LJ14) 104 119 64: 280 type=193 (LJ14) 105 107 64: 281 type=193 (LJ14) 105 108 64: 282 type=191 (LJ14) 105 109 64: 283 type=194 (LJ14) 105 116 64: 284 type=186 (LJ14) 105 117 64: 285 type=195 (LJ14) 106 113 64: 286 type=195 (LJ14) 106 114 64: 287 type=195 (LJ14) 106 116 64: 288 type=187 (LJ14) 106 117 64: 289 type=193 (LJ14) 107 110 64: 290 type=193 (LJ14) 107 111 64: 291 type=196 (LJ14) 107 112 64: 292 type=196 (LJ14) 107 115 64: 293 type=193 (LJ14) 108 110 64: 294 type=193 (LJ14) 108 111 64: 295 type=196 (LJ14) 108 112 64: 296 type=196 (LJ14) 108 115 64: 297 type=197 (LJ14) 109 115 64: 298 type=194 (LJ14) 110 113 64: 299 type=194 (LJ14) 110 114 64: 300 type=194 (LJ14) 111 113 64: 301 type=194 (LJ14) 111 114 64: 302 type=196 (LJ14) 115 120 64: 303 type=197 (LJ14) 115 121 64: 304 type=198 (LJ14) 115 134 64: 305 type=190 (LJ14) 116 118 64: 306 type=195 (LJ14) 116 119 64: 307 type=186 (LJ14) 117 122 64: 308 type=186 (LJ14) 117 123 64: 309 type=187 (LJ14) 117 124 64: 310 type=188 (LJ14) 117 135 64: 311 type=189 (LJ14) 117 136 64: 312 type=190 (LJ14) 118 120 64: 313 type=190 (LJ14) 118 121 64: 314 type=190 (LJ14) 118 134 64: 315 type=191 (LJ14) 119 125 64: 316 type=192 (LJ14) 119 126 64: 317 type=192 (LJ14) 119 130 64: 318 type=190 (LJ14) 119 137 64: 319 type=192 (LJ14) 119 138 64: 320 type=193 (LJ14) 120 122 64: 321 type=193 (LJ14) 120 123 64: 322 type=191 (LJ14) 120 124 64: 323 type=194 (LJ14) 120 135 64: 324 type=186 (LJ14) 120 136 64: 325 type=191 (LJ14) 121 127 64: 326 type=191 (LJ14) 121 128 64: 327 type=191 (LJ14) 121 129 64: 328 type=191 (LJ14) 121 131 64: 329 type=191 (LJ14) 121 132 64: 330 type=191 (LJ14) 121 133 64: 331 type=195 (LJ14) 121 135 64: 332 type=187 (LJ14) 121 136 64: 333 type=193 (LJ14) 122 125 64: 334 type=191 (LJ14) 122 126 64: 335 type=191 (LJ14) 122 130 64: 336 type=196 (LJ14) 122 134 64: 337 type=193 (LJ14) 123 125 64: 338 type=191 (LJ14) 123 126 64: 339 type=191 (LJ14) 123 130 64: 340 type=196 (LJ14) 123 134 64: 341 type=197 (LJ14) 124 134 64: 342 type=193 (LJ14) 125 127 64: 343 type=193 (LJ14) 125 128 64: 344 type=193 (LJ14) 125 129 64: 345 type=193 (LJ14) 125 131 64: 346 type=193 (LJ14) 125 132 64: 347 type=193 (LJ14) 125 133 64: 348 type=191 (LJ14) 126 131 64: 349 type=191 (LJ14) 126 132 64: 350 type=191 (LJ14) 126 133 64: 351 type=191 (LJ14) 127 130 64: 352 type=191 (LJ14) 128 130 64: 353 type=191 (LJ14) 129 130 64: 354 type=196 (LJ14) 134 139 64: 355 type=197 (LJ14) 134 140 64: 356 type=198 (LJ14) 134 144 64: 357 type=190 (LJ14) 135 137 64: 358 type=195 (LJ14) 135 138 64: 359 type=186 (LJ14) 136 141 64: 360 type=186 (LJ14) 136 142 64: 361 type=186 (LJ14) 136 143 64: 362 type=188 (LJ14) 136 145 64: 363 type=189 (LJ14) 136 146 64: 364 type=190 (LJ14) 137 139 64: 365 type=190 (LJ14) 137 140 64: 366 type=190 (LJ14) 137 144 64: 367 type=190 (LJ14) 138 147 64: 368 type=192 (LJ14) 138 148 64: 369 type=193 (LJ14) 139 141 64: 370 type=193 (LJ14) 139 142 64: 371 type=193 (LJ14) 139 143 64: 372 type=194 (LJ14) 139 145 64: 373 type=186 (LJ14) 139 146 64: 374 type=195 (LJ14) 140 145 64: 375 type=187 (LJ14) 140 146 64: 376 type=196 (LJ14) 141 144 64: 377 type=196 (LJ14) 142 144 64: 378 type=196 (LJ14) 143 144 64: 379 type=196 (LJ14) 144 149 64: 380 type=197 (LJ14) 144 150 64: 381 type=198 (LJ14) 144 154 64: 382 type=190 (LJ14) 145 147 64: 383 type=195 (LJ14) 145 148 64: 384 type=186 (LJ14) 146 151 64: 385 type=186 (LJ14) 146 152 64: 386 type=186 (LJ14) 146 153 64: 387 type=188 (LJ14) 146 155 64: 388 type=190 (LJ14) 147 149 64: 389 type=190 (LJ14) 147 150 64: 390 type=190 (LJ14) 147 154 64: 391 type=193 (LJ14) 149 151 64: 392 type=193 (LJ14) 149 152 64: 393 type=193 (LJ14) 149 153 64: 394 type=194 (LJ14) 149 155 64: 395 type=195 (LJ14) 150 155 64: 396 type=196 (LJ14) 151 154 64: 397 type=196 (LJ14) 152 154 64: 398 type=196 (LJ14) 153 154 64: Coulomb-14: 64: nr: 0 64: LJC-14 q: 64: nr: 0 64: LJC Pairs NB: 64: nr: 0 64: LJ (SR): 64: nr: 0 64: Buck.ham (SR): 64: nr: 0 64: LJ: 64: nr: 0 64: B.ham: 64: nr: 0 64: Disper. corr.: 64: nr: 0 64: Coulomb (SR): 64: nr: 0 64: Coul: 64: nr: 0 64: RF excl.: 64: nr: 0 64: Coul. recip.: 64: nr: 0 64: LJ recip.: 64: nr: 0 64: DPD: 64: nr: 0 64: Polarization: 64: nr: 0 64: Water Pol.: 64: nr: 0 64: Thole Pol.: 64: nr: 0 64: Anharm. Pol.: 64: nr: 0 64: Position Rest.: 64: nr: 0 64: Flat-b. P-R.: 64: nr: 0 64: Dis. Rest.: 64: nr: 0 64: D.R.Viol. (nm): 64: nr: 0 64: Orient. Rest.: 64: nr: 0 64: Ori. R. RMSD: 64: nr: 0 64: Angle Rest.: 64: nr: 0 64: Angle Rest. Z: 64: nr: 0 64: Dih. Rest.: 64: nr: 0 64: Dih. Rest. Vi.: 64: nr: 0 64: Constraint: 64: nr: 0 64: Constr. No Co.: 64: nr: 0 64: Settle: 64: nr: 0 64: Virtual site 1: 64: nr: 0 64: Virtual site 2: 64: nr: 0 64: Virt. site 2fd: 64: nr: 0 64: Virtual site 3: 64: nr: 0 64: Virt. site 3fd: 64: nr: 0 64: Vir. site 3fad: 64: nr: 0 64: Vir. site 3out: 64: nr: 0 64: Virt. site 4fd: 64: nr: 0 64: Vir. site 4fdn: 64: nr: 0 64: Virtual site N: 64: nr: 0 64: COM Pull En.: 64: nr: 0 64: Dens. fitting: 64: nr: 0 64: Quantum En.: 64: nr: 0 64: NN Potential: 64: nr: 0 64: Potential: 64: nr: 0 64: Kinetic En.: 64: nr: 0 64: Total Energy: 64: nr: 0 64: Conserved En.: 64: nr: 0 64: Temperature: 64: nr: 0 64: Vir. Temp.: 64: nr: 0 64: Pres. DC: 64: nr: 0 64: Pressure: 64: nr: 0 64: dH/dl constr.: 64: nr: 0 64: dVremain/dl: 64: nr: 0 64: dEkin/dl: 64: nr: 0 64: dVcoul/dl: 64: nr: 0 64: dVvdw/dl: 64: nr: 0 64: dVbonded/dl: 64: nr: 0 64: dVrestraint/dl: 64: nr: 0 64: dVtemp/dl: 64: nr: 0 64: grp[T-Coupling ] nr=1, name=[ rest] 64: grp[Energy Mon. ] nr=1, name=[ rest] 64: grp[Acc. not used] nr=1, name=[ rest] 64: grp[Freeze ] nr=1, name=[ rest] 64: grp[User1 ] nr=1, name=[ rest] 64: grp[User2 ] nr=1, name=[ rest] 64: grp[VCM ] nr=1, name=[ rest] 64: grp[Compressed X] nr=1, name=[ rest] 64: grp[Or. Res. Fit] nr=1, name=[ rest] 64: grp[QMMM ] nr=1, name=[ rest] 64: grpname (11): 64: grpname[0]={name="System"} 64: grpname[1]={name="Protein"} 64: grpname[2]={name="Protein-H"} 64: grpname[3]={name="C-alpha"} 64: grpname[4]={name="Backbone"} 64: grpname[5]={name="MainChain"} 64: grpname[6]={name="MainChain+Cb"} 64: grpname[7]={name="MainChain+H"} 64: grpname[8]={name="SideChain"} 64: grpname[9]={name="SideChain-H"} 64: grpname[10]={name="rest"} 64: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 64: allocated 0 0 0 0 0 0 0 0 0 0 64: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 64: box (3x3): 64: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 64: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 64: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 64: box_rel (3x3): 64: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: boxv (3x3): 64: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: pres_prev (3x3): 64: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: svir_prev (3x3): 64: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: fvir_prev (3x3): 64: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: nosehoover_xi: not available 64: x (156x3): 64: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 64: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 64: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 64: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 64: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 64: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 64: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 64: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 64: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 64: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 64: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 64: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 64: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 64: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 64: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 64: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 64: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 64: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 64: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 64: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 64: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 64: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 64: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 64: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 64: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 64: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 64: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 64: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 64: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 64: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 64: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 64: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 64: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 64: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 64: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 64: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 64: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 64: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 64: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 64: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 64: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 64: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 64: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 64: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 64: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 64: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 64: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 64: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 64: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 64: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 64: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 64: x[ 51]={ 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0.00000e+00} 64: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 64: Group statistics 64: T-Coupling : 156 (total 156 atoms) 64: Energy Mon. : 156 (total 156 atoms) 64: Acc. not used: 156 (total 156 atoms) 64: Freeze : 156 (total 156 atoms) 64: User1 : 156 (total 156 atoms) 64: User2 : 156 (total 156 atoms) 64: VCM : 156 (total 156 atoms) 64: Compressed X: 156 (total 156 atoms) 64: Or. Res. Fit: 156 (total 156 atoms) 64: QMMM : 156 (total 156 atoms) 64: [ OK ] DumpTest.WorksWithTpr (6 ms) 64: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 64: [----------] 2 tests from DumpTest (7 ms total) 64: 64: [----------] 3 tests from HelpwritingTest 64: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 64: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 64: [ RUN ] HelpwritingTest.DumpWritesHelp 64: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 64: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 64: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 64: [----------] 3 tests from HelpwritingTest (0 ms total) 64: 64: [----------] 7 tests from GmxMakeNdx 64: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 64: 64: Reading structure file 64: Going to read 0 old index file(s) 64: Analysing residue names: 64: There are: 16 Protein residues 64: Analysing Protein... 64: 64: 0 System : 256 atoms 64: 1 Protein : 256 atoms 64: 2 Protein-H : 139 atoms 64: 3 C-alpha : 16 atoms 64: 4 Backbone : 48 atoms 64: 5 MainChain : 63 atoms 64: 6 MainChain+Cb : 78 atoms 64: 7 MainChain+H : 81 atoms 64: 8 SideChain : 175 atoms 64: 9 SideChain-H : 76 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) 64: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 64: Going to read 1 old index file(s) 64: Deducing 22 atoms in the system from indices in the index file 64: 64: 0 System : 22 atoms 64: 1 Protein : 22 atoms 64: 2 Protein-H : 10 atoms 64: 3 C-alpha : 1 atoms 64: 4 Backbone : 5 atoms 64: 5 MainChain : 7 atoms 64: 6 MainChain+Cb : 8 atoms 64: 7 MainChain+H : 9 atoms 64: 8 SideChain : 13 atoms 64: 9 SideChain-H : 3 atoms 64: 10 CA : 1 atoms 64: 11 C_&_r_1 : 1 atoms 64: 12 C_&_r_2 : 1 atoms 64: 13 N_&_r_2 : 1 atoms 64: 14 N_&_r_3 : 1 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: Copied index group 1 'Protein' 64: Copied index group 2 'Protein-H' 64: Merged two groups with OR: 22 10 -> 22 64: 64: > 64: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 64: [ RUN ] GmxMakeNdx.HandlesNotProtein 64: Going to read 1 old index file(s) 64: Deducing 6 atoms in the system from indices in the index file 64: 64: 0 System : 6 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 64: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 64: Going to read 1 old index file(s) 64: Deducing 22 atoms in the system from indices in the index file 64: 64: 0 System : 22 atoms 64: 1 Protein : 22 atoms 64: 2 Protein-H : 10 atoms 64: 3 C-alpha : 1 atoms 64: 4 Backbone : 5 atoms 64: 5 MainChain : 7 atoms 64: 6 MainChain+Cb : 8 atoms 64: 7 MainChain+H : 9 atoms 64: 8 SideChain : 13 atoms 64: 9 SideChain-H : 3 atoms 64: 10 CA : 1 atoms 64: 11 C_&_r_1 : 1 atoms 64: 12 C_&_r_2 : 1 atoms 64: 13 N_&_r_2 : 1 atoms 64: 14 N_&_r_3 : 1 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: Copied index group 4 'Backbone' 64: Copied index group 8 'SideChain' 64: Merged two groups with AND: 5 13 -> 0 64: Group is empty 64: 64: > 64: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 64: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 64: Going to read 1 old index file(s) 64: Deducing 6 atoms in the system from indices in the index file 64: 64: 0 System : 6 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: Removed group 0 'System' 64: 64: > 64: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 64: [ RUN ] GmxMakeNdx.Splitres 64: 64: Reading structure file 64: Going to read 0 old index file(s) 64: Analysing residue names: 64: There are: 2 Water residues 64: 64: 0 System : 6 atoms 64: 1 Water : 6 atoms 64: 2 SOL : 6 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: Splitting group 1 'Water' into residues 64: 64: > 64: [ OK ] GmxMakeNdx.Splitres (0 ms) 64: [ RUN ] GmxMakeNdx.Splitat 64: 64: Reading structure file 64: Going to read 0 old index file(s) 64: Analysing residue names: 64: There are: 2 Water residues 64: 64: 0 System : 6 atoms 64: 1 Water : 6 atoms 64: 2 SOL : 6 atoms 64: 64: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 64: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 64: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 64: 'r': residue 'res' nr 'chain' char 64: "name": group 'case': case sensitive 'q': save and quit 64: 'ri': residue index 64: 64: > 64: Splitting group 1 'Water' into atoms 64: 64: > 64: [ OK ] GmxMakeNdx.Splitat (0 ms) 64: [----------] 7 tests from GmxMakeNdx (6 ms total) 64: 64: [----------] 4 tests from ReportMethodsTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Setting the LD random seed to -134228737 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 64: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 64: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 64: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 64: [ RUN ] ReportMethodsTest.WritesCorrectInformation 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 64: [ RUN ] ReportMethodsTest.ToolEndToEndTest 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: section: Methods 64: subsection: Simulation system 64: A system of 1 molecules (156 atoms) was simulated. 64: 64: subsection: Simulation settings 64: A total of 0 ns were simulated with a time step of 1 fs. 64: Neighbor searching was performed every 10 steps. 64: The Cut-off algorithm was used for electrostatic interactions. 64: with a cut-off of 1 nm. 64: A single cut-off of 1.1 nm was used for Van der Waals interactions. 64: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 64: [----------] 4 tests from ReportMethodsTest (0 ms total) 64: 64: [----------] 4 tests from ConvertTprTest 64: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting the LD random seed to 2113666814 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: Input file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 0 64: Runtime for the run 0 ps 64: Run end step 0 64: Run end time 0 ps 64: 64: Extending remaining runtime by 100 ps 64: 64: Output file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 100000 64: Runtime for the run 100 ps 64: Run end step 100000 64: Run end time 100 ps 64: 64: Input file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 100000 64: Runtime for the run 100 ps 64: Run end step 100000 64: Run end time 100 ps 64: 64: Extending remaining runtime by 100 ps 64: 64: Output file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 200000 64: Runtime for the run 200 ps 64: Run end step 200000 64: Run end time 200 ps 64: 64: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (169 ms) 64: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting the LD random seed to -268438817 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: Input file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 0 64: Runtime for the run 0 ps 64: Run end step 0 64: Run end time 0 ps 64: 64: Extending remaining runtime to 100 ps 64: 64: Output file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 100000 64: Runtime for the run 100 ps 64: Run end step 100000 64: Run end time 100 ps 64: 64: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (167 ms) 64: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting nsteps to 102 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting the LD random seed to -966263139 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: Input file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 0 64: Runtime for the run 0 ps 64: Run end step 0 64: Run end time 0 ps 64: 64: 64: Output file: 64: Run start step 0 64: Run start time 0 ps 64: Step to be made during run 102 64: Runtime for the run 0.102 ps 64: Run end step 102 64: Run end time 0.102 ps 64: 64: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (166 ms) 64: [ RUN ] ConvertTprTest.generateVelocitiesTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting the LD random seed to -1174962498 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] ConvertTprTest.generateVelocitiesTest (165 ms) 64: [----------] 4 tests from ConvertTprTest (668 ms total) 64: 64: [----------] 1 test from ConvertTprNoVelocityTest 64: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file lysozyme.top, line 1465]: 64: System has non-zero total charge: 2.000000 64: Total charge should normally be an integer. See 64: https://manual.gromacs.org/current/user-guide/floating-point.html 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: 64: NOTE 3 [file lysozyme.top, line 1465]: 64: Zero-step energy minimization will alter the coordinates before 64: calculating the energy. If you just want the energy of a single point, 64: try zero-step MD (with unconstrained_start = yes). To do multiple 64: single-point energy evaluations of different configurations of the same 64: topology, use mdrun -rerun. 64: 64: Number of degrees of freedom in T-Coupling group rest is 465.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 64: Setting the LD random seed to -1350639938 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 64: Analysing residue names: 64: There are: 10 Protein residues 64: Analysing Protein... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (163 ms) 64: [----------] 1 test from ConvertTprNoVelocityTest (163 ms total) 64: 64: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: trr version: GMX_trn_file (single precision) 64: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 64: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 64: Will write trr: Trajectory in portable xdr format 64: Group 0 ( System) has 6 elements 64: Group 1 (FirstWaterMolecule) has 3 elements 64: Group 2 (SecondWaterMolecule) has 3 elements 64: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 64: -> frame 1 time 1.000 64: Last written: frame 1 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: Select group for output 64: Selected 2: 'SecondWaterMolecule' 64: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 64: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (4 ms total) 64: 64: [----------] 30 tests from Works/TrjconvDumpTest 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 64: Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 64: Precision of /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 64: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 64: Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 0 ps 64: -> frame 0 time 0.000 64: Last written: frame 0 time 0.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 64: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 64: Will write trr: Trajectory in portable xdr format 64: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 64: 64: Dumping frame at t= 1 ps 64: -> frame 0 time 1.000 64: Last written: frame 0 time 1.000 64: 64: 64: Note that major changes are planned in future for trjconv, to improve usability and utility. 64: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 64: [----------] 30 tests from Works/TrjconvDumpTest (8 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 63 tests from 8 test suites ran. (1199 ms total) 64: [ PASSED ] 63 tests. 64/96 Test #64: ToolUnitTests ................................ Passed 1.39 sec test 65 Start 65: ToolWithLeaksUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/ToolWithLeaksUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests 65: Test timeout computed to be: 1920 65: [==========] Running 2 tests from 2 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from ConvertTprTest 65: [ RUN ] ConvertTprTest.selectIndexTest 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file lysozyme.top, line 1465]: 65: System has non-zero total charge: 2.000000 65: Total charge should normally be an integer. See 65: https://manual.gromacs.org/current/user-guide/floating-point.html 65: for discussion on how close it should be to an integer. 65: 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 465.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Group 0 ( System) has 156 elements 65: Group 1 ( Protein) has 156 elements 65: Group 2 ( Protein-H) has 75 elements 65: Group 3 ( C-alpha) has 10 elements 65: Group 4 ( Backbone) has 30 elements 65: Group 5 ( MainChain) has 40 elements 65: Group 6 ( MainChain+Cb) has 49 elements 65: Group 7 ( MainChain+H) has 52 elements 65: Group 8 ( SideChain) has 104 elements 65: Group 9 ( SideChain-H) has 35 elements 65: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 65: Reduced ilist BONDS from 156 to 75 entries 65: Reduced ilist ANGLES from 281 to 98 entries 65: Reduced ilist PDIHS from 29 to 12 entries 65: Reduced ilist RBDIHS from 313 to 89 entries 65: Reduced ilist LJ14 from 399 to 107 entries 65: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Setting the LD random seed to -1956714509 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 65: Analysing residue names: 65: There are: 10 Protein residues 65: Analysing Protein... 65: 65: This run will generate roughly 0 Mb of data 65: Selected 2: 'Protein-H' 65: [ OK ] ConvertTprTest.selectIndexTest (170 ms) 65: [----------] 1 test from ConvertTprTest (170 ms total) 65: 65: [----------] 1 test from ConvertTprNoVelocityTest 65: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file lysozyme.top, line 1465]: 65: System has non-zero total charge: 2.000000 65: Total charge should normally be an integer. See 65: https://manual.gromacs.org/current/user-guide/floating-point.html 65: for discussion on how close it should be to an integer. 65: 65: 65: 65: 65: NOTE 3 [file lysozyme.top, line 1465]: 65: Zero-step energy minimization will alter the coordinates before 65: calculating the energy. If you just want the energy of a single point, 65: try zero-step MD (with unconstrained_start = yes). To do multiple 65: single-point energy evaluations of different configurations of the same 65: topology, use mdrun -rerun. 65: 65: Number of degrees of freedom in T-Coupling group rest is 465.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Group 0 ( System) has 156 elements 65: Group 1 ( Protein) has 156 elements 65: Group 2 ( Protein-H) has 75 elements 65: Group 3 ( C-alpha) has 10 elements 65: Group 4 ( Backbone) has 30 elements 65: Group 5 ( MainChain) has 40 elements 65: Group 6 ( MainChain+Cb) has 49 elements 65: Group 7 ( MainChain+H) has 52 elements 65: Group 8 ( SideChain) has 104 elements 65: Group 9 ( SideChain-H) has 35 elements 65: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 65: Reduced ilist BONDS from 156 to 75 entries 65: Reduced ilist ANGLES from 281 to 98 entries 65: Reduced ilist PDIHS from 29 to 12 entries 65: Reduced ilist RBDIHS from 313 to 89 entries 65: Reduced ilist LJ14 from 399 to 107 entries 65: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 65: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 65: Setting the LD random seed to -41958854 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 65: Analysing residue names: 65: There are: 10 Protein residues 65: Analysing Protein... 65: 65: This run will generate roughly 0 Mb of data 65: Selected 2: 'Protein-H' 65: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (157 ms) 65: [----------] 1 test from ConvertTprNoVelocityTest (157 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 2 test suites ran. (327 ms total) 65: [ PASSED ] 2 tests. 65/96 Test #65: ToolWithLeaksUnitTests ....................... Passed 0.52 sec test 66 Start 66: FileIOTests 66: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/FileIOTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/fileio/tests 66: Test timeout computed to be: 30 66: [==========] Running 421 tests from 17 test suites. 66: [----------] Global test environment set-up. 66: [----------] 4 tests from Checkpoint 66: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 66: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 66: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 66: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 66: [ RUN ] Checkpoint.KvtRoundTripInt64 66: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 66: [ RUN ] Checkpoint.KvtRoundTripReal 66: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 66: [----------] 4 tests from Checkpoint (0 ms total) 66: 66: [----------] 1 test from StructureIOTest 66: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 66: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 66: [----------] 1 test from StructureIOTest (0 ms total) 66: 66: [----------] 2 tests from FileMD5Test 66: [ RUN ] FileMD5Test.CanComputeMD5 66: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 66: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 66: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 66: [----------] 2 tests from FileMD5Test (0 ms total) 66: 66: [----------] 4 tests from FileTypeTest 66: [ RUN ] FileTypeTest.CorrectValueForEmptyString 66: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 66: [ RUN ] FileTypeTest.CorrectValueForNoExtension 66: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 66: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 66: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 66: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 66: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 66: [----------] 4 tests from FileTypeTest (0 ms total) 66: 66: [----------] 4 tests from ColorMapTest 66: [ RUN ] ColorMapTest.CanReadFromFile 66: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 66: [ RUN ] ColorMapTest.CanWriteToFile 66: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 66: [ RUN ] ColorMapTest.RoundTrip 66: [ OK ] ColorMapTest.RoundTrip (0 ms) 66: [ RUN ] ColorMapTest.SearchWorks 66: [ OK ] ColorMapTest.SearchWorks (0 ms) 66: [----------] 4 tests from ColorMapTest (0 ms total) 66: 66: [----------] 4 tests from MatioTest 66: [ RUN ] MatioTest.CanWriteToFile 66: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 66: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 66: Converted a 4x3 matrix with 4 levels to reals 66: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 66: [ RUN ] MatioTest.CanConvertToNewRealMatrix 66: Converted a 4x3 matrix with 4 levels to reals 66: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 66: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 66: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (1 ms) 66: [----------] 4 tests from MatioTest (1 ms total) 66: 66: [----------] 3 tests from MrcSerializer 66: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 66: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 66: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 66: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 66: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 66: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 66: [----------] 3 tests from MrcSerializer (0 ms total) 66: 66: [----------] 4 tests from MrcDensityMap 66: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 66: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 66: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 66: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 66: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 66: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 66: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 66: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 66: [----------] 4 tests from MrcDensityMap (1 ms total) 66: 66: [----------] 8 tests from MrcDensityMapHeaderTest 66: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 66: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 66: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 66: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 66: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 66: [ RUN ] MrcDensityMapHeaderTest.IsSane 66: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 66: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 66: 66: [----------] 10 tests from ReadTest 66: [ RUN ] ReadTest.get_eint_ReadsInteger 66: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 66: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 66: 66: ERROR 1 [file unknown]: 66: Right hand side '0.8' for parameter 'test' in parameter file is not an 66: integer value 66: 66: 66: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 66: [ RUN ] ReadTest.get_eint_WarnsAboutString 66: 66: ERROR 1 [file unknown]: 66: Right hand side 'hello' for parameter 'test' in parameter file is not an 66: integer value 66: 66: 66: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 66: [ RUN ] ReadTest.get_eint64_ReadsInteger 66: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 66: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 66: 66: ERROR 1 [file unknown]: 66: Right hand side '0.8' for parameter 'test' in parameter file is not an 66: integer value 66: 66: 66: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 66: [ RUN ] ReadTest.get_eint64_WarnsAboutString 66: 66: ERROR 1 [file unknown]: 66: Right hand side 'hello' for parameter 'test' in parameter file is not an 66: integer value 66: 66: 66: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 66: [ RUN ] ReadTest.get_ereal_ReadsInteger 66: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 66: [ RUN ] ReadTest.get_ereal_ReadsFloat 66: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 66: [ RUN ] ReadTest.get_ereal_WarnsAboutString 66: 66: ERROR 1 [file unknown]: 66: Right hand side 'hello' for parameter 'test' in parameter file is not a 66: real value 66: 66: 66: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 66: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 66: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 66: [----------] 10 tests from ReadTest (0 ms total) 66: 66: [----------] 3 tests from TimeControlTest 66: [ RUN ] TimeControlTest.UnSetHasNoValue 66: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 66: [ RUN ] TimeControlTest.CanSetValue 66: [ OK ] TimeControlTest.CanSetValue (0 ms) 66: [ RUN ] TimeControlTest.CanUnsetValueAgain 66: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 66: [----------] 3 tests from TimeControlTest (0 ms total) 66: 66: [----------] 1 test from FileIOXdrSerializerTest 66: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 66: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 66: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 66: 66: [----------] 1 test from TngTest 66: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 66: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 66: [----------] 1 test from TngTest (0 ms total) 66: 66: [----------] 4 tests from XvgioTest 66: [ RUN ] XvgioTest.readXvgIntWorks 66: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 66: [ RUN ] XvgioTest.readXvgRealWorks 66: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 66: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 66: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 66: [ RUN ] XvgioTest.readXvgDeprecatedWorks 66: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 66: [----------] 4 tests from XvgioTest (0 ms total) 66: 66: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 66: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 66: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 66: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 66: 66: [----------] 360 tests from FileTypeMatch/FileTypeTest 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 66: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 66: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 66: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 66: 66: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 66: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 66: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 66: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 421 tests from 17 test suites ran. (7 ms total) 66: [ PASSED ] 421 tests. 66/96 Test #66: FileIOTests .................................. Passed 0.12 sec test 67 Start 67: SelectionUnitTests 67: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/tests 67: Test timeout computed to be: 30 67: [==========] Running 201 tests from 11 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from IndexGroupTest 67: [ RUN ] IndexGroupTest.RemovesDuplicates 67: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 67: [----------] 1 test from IndexGroupTest (0 ms total) 67: 67: [----------] 15 tests from IndexBlockTest 67: [ RUN ] IndexBlockTest.CreatesUnknownBlock 67: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 67: [ RUN ] IndexBlockTest.CreatesAtomBlock 67: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 67: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 67: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 67: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 67: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 67: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 67: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 67: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 67: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 67: [ RUN ] IndexBlockTest.CreatesSingleBlock 67: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 67: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 67: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 67: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 67: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 67: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 67: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 67: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 67: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 67: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 67: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 67: [----------] 15 tests from IndexBlockTest (0 ms total) 67: 67: [----------] 11 tests from IndexMapTest 67: [ RUN ] IndexMapTest.InitializesAtomBlock 67: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 67: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 67: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 67: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 67: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 67: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 67: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 67: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 67: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 67: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 67: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 67: [ RUN ] IndexMapTest.InitializesMoleculeBlock 67: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 67: [ RUN ] IndexMapTest.MapsSingleBlock 67: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 67: [ RUN ] IndexMapTest.MapsResidueBlocks 67: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 67: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 67: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 67: [ RUN ] IndexMapTest.HandlesMultipleRequests 67: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 67: [----------] 11 tests from IndexMapTest (1 ms total) 67: 67: [----------] 3 tests from IndexGroupsAndNamesTest 67: [ RUN ] IndexGroupsAndNamesTest.containsNames 67: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 67: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 67: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 67: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 67: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 67: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 67: 67: [----------] 15 tests from NeighborhoodSearchTest 67: [ RUN ] NeighborhoodSearchTest.SimpleSearch 67: [ OK ] NeighborhoodSearchTest.SimpleSearch (8 ms) 67: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 67: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (8 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearchBox 67: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 67: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 67: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 67: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 67: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 67: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 67: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 67: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (25 ms) 67: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 67: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 67: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 67: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 67: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 67: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 67: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 67: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 67: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 67: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 67: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 67: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 67: [----------] 15 tests from NeighborhoodSearchTest (54 ms total) 67: 67: [----------] 13 tests from PositionCalculationTest 67: [ RUN ] PositionCalculationTest.ComputesAtomPositions 67: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 67: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 67: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 67: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 67: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 67: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 67: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 67: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 67: [ RUN ] PositionCalculationTest.ComputesPositionMask 67: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 67: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 67: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 67: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 67: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 67: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 67: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 67: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 67: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 67: [----------] 13 tests from PositionCalculationTest (1 ms total) 67: 67: [----------] 33 tests from SelectionCollectionTest 67: [ RUN ] SelectionCollectionTest.HandlesNoSelections 67: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 67: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 67: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 67: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 67: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 67: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 67: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 67: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 67: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 67: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 67: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 67: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 67: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 67: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 67: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 67: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 67: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 67: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 67: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 67: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 67: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 67: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 67: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 67: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 67: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 67: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 67: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 67: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 67: [----------] 33 tests from SelectionCollectionTest (6 ms total) 67: 67: [----------] 14 tests from SelectionCollectionInteractiveTest 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 67: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 67: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 67: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 67: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 67: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 67: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 67: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 67: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 67: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 67: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 67: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 67: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 67: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 67: [----------] 14 tests from SelectionCollectionInteractiveTest (3 ms total) 67: 67: [----------] 70 tests from SelectionCollectionDataTest 67: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 67: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 67: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesResnr 67: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 67: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 67: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 67: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 67: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 67: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesChain 67: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesMass 67: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesCharge 67: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 67: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 67: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 67: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesBeta 67: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesResname 67: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 67: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 67: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 67: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 67: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 67: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 67: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 67: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 67: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 67: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 67: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 67: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 67: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 67: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 67: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 67: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 67: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 67: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 67: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 67: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 67: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 67: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 67: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 67: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 67: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 67: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 67: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 67: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 67: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 67: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 67: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 67: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 67: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 67: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 67: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 67: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 67: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 67: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 67: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 67: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 67: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 67: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 67: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 67: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 67: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 67: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 67: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 67: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 67: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 67: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 67: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 67: [----------] 70 tests from SelectionCollectionDataTest (31 ms total) 67: 67: [----------] 17 tests from SelectionOptionTest 67: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 67: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 67: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 67: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 67: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 67: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 67: [ RUN ] SelectionOptionTest.ChecksEmptySelections 67: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 67: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 67: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesTooManySelections 67: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 67: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 67: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesAdjuster 67: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 67: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 67: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 67: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 67: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 67: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 67: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 67: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 67: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 67: [----------] 17 tests from SelectionOptionTest (2 ms total) 67: 67: [----------] 9 tests from SelectionFileOptionTest 67: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 67: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 67: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 67: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 67: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 67: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 67: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 67: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 67: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 67: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 67: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 67: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 67: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 67: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 201 tests from 11 test suites ran. (104 ms total) 67: [ PASSED ] 201 tests. 67/96 Test #67: SelectionUnitTests ........................... Passed 0.43 sec test 68 Start 68: MdrunOutputTests 68: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 12 tests from 5 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from MdrunTest 68: [ RUN ] MdrunTest.WritesHelp 68: [ OK ] MdrunTest.WritesHelp (5 ms) 68: [----------] 1 test from MdrunTest (5 ms total) 68: 68: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1351090309 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.064 0.032 199.6 68: (ns/day) (hour/ns) 68: Performance: 5.395 4.448 68: Reading frame 0 time 0.000 68: # Atoms 6 68: Reading frame 1 time 0.001 Last frame 1 time 0.001 68: 68: 68: Item #frames Timestep (ps) 68: Step 2 0.001 68: Time 2 0.001 68: Lambda 0 68: Coords 2 0.001 68: Velocities 0 68: Forces 0 68: Box 2 0.001 68: Checking file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (72 ms) 68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -1749123329 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.008 0.004 196.9 68: (ns/day) (hour/ns) 68: Performance: 42.437 0.566 68: Reading frame 0 time 0.000 68: # Atoms 6 68: Reading frame 1 time 0.001 Last frame 1 time 0.001 68: 68: 68: Item #frames Timestep (ps) 68: Step 2 0.001 68: Time 2 0.001 68: Lambda 0 68: Coords 2 0.001 68: Velocities 0 68: Forces 0 68: Box 2 0.001 68: Checking file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (31 ms) 68: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -134479878 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.056 0.028 199.5 68: (ns/day) (hour/ns) 68: Performance: 6.145 3.905 68: Reading frame 0 time 0.000 68: # Atoms 3 68: Reading frame 1 time 0.001 Last frame 1 time 0.001 68: 68: 68: Item #frames Timestep (ps) 68: Step 2 0.001 68: Time 2 0.001 68: Lambda 0 68: Coords 2 0.001 68: Velocities 0 68: Forces 0 68: Box 2 0.001 68: Checking file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 68: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (76 ms) 68: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (180 ms total) 68: 68: [----------] 2 tests from Argon12/OutputFiles 68: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.7 68: (ns/day) (hour/ns) 68: Performance: 30.710 0.782 68: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (51 ms) 68: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 46 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.176 0.088 199.9 68: (ns/day) (hour/ns) 68: Performance: 16.674 1.439 68: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (120 ms) 68: [----------] 2 tests from Argon12/OutputFiles (171 ms total) 68: 68: [----------] 3 tests from MdrunCanWrite/Trajectories 68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 6 steps, 0.0 ps. 68: Setting the LD random seed to -346427461 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 50 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.160 0.080 199.9 68: (ns/day) (hour/ns) 68: Performance: 7.539 3.183 68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (159 ms) 68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 6 steps, 0.0 ps. 68: Setting the LD random seed to -271589413 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 33 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.048 199.8 68: (ns/day) (hour/ns) 68: Performance: 12.534 1.915 68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (132 ms) 68: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 6 steps, 0.0 ps. 68: Setting the LD random seed to -34681345 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.013 0.007 198.4 68: (ns/day) (hour/ns) 68: Performance: 89.868 0.267 68: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (34 ms) 68: [----------] 3 tests from MdrunCanWrite/Trajectories (326 ms total) 68: 68: [----------] 3 tests from MdrunCanWrite/NptTrajectories 68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 667672559 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 199.1 68: (ns/day) (hour/ns) 68: Performance: 21.314 1.126 68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (37 ms) 68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: We recommend using the C-rescale barostat instead. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: 68: There was 1 WARNING 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 788491757 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 78 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.112 0.056 199.8 68: (ns/day) (hour/ns) 68: Performance: 4.608 5.208 68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (135 ms) 68: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -113290882 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 60 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.120 0.060 199.8 68: (ns/day) (hour/ns) 68: Performance: 4.304 5.576 68: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (147 ms) 68: [----------] 3 tests from MdrunCanWrite/NptTrajectories (321 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 12 tests from 5 test suites ran. (1021 ms total) 68: [ PASSED ] 12 tests. 68/96 Test #68: MdrunOutputTests ............................. Passed 1.17 sec test 69 Start 69: MdrunModulesTests 69: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 15 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 9 tests from DensityFittingTest 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 2 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 3 steps. 69: Potential Energy = -3.8565254e+03 69: Maximum force = 4.5099883e+03 on atom 3 69: Norm of force = 1.6816849e+03 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -3146429 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (5 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 2 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 3 steps. 69: Potential Energy = -9.8207725e+03 69: Maximum force = 7.3954834e+03 on atom 2 69: Norm of force = 2.7825089e+03 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2079322589 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (16 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Overriding nsteps with value passed on the command line: 4 steps 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -5.4739321e+03 69: Maximum force = 6.1322017e+03 on atom 2 69: Norm of force = 1.7702150e+03 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1560952889 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (25 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 2 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 3 steps. 69: Potential Energy = -3.8565254e+03 69: Maximum force = 4.5099883e+03 on atom 3 69: Norm of force = 1.6816849e+03 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -546848790 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (16 ms) 69: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 2 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 3 steps. 69: Potential Energy = -2.7138664e+04 69: Maximum force = 6.7827656e+03 on atom 2 69: Norm of force = 1.9608866e+03 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -276890691 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (16 ms) 69: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 69: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 69: [ RUN ] DensityFittingTest.CheckpointWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (2) 69: 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -411312393 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.030 0.015 199.4 69: (ns/day) (hour/ns) 69: Performance: 17.166 1.398 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.019 199.6 69: (ns/day) (hour/ns) 69: Performance: 22.798 1.053 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (43 ms) 69: [----------] 9 tests from DensityFittingTest (124 ms total) 69: 69: [----------] 4 tests from MimicTest 69: [ RUN ] MimicTest.OneQuantumMol 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 21.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 69: 69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.009 0.005 199.1 69: (ns/day) (hour/ns) 69: Performance: 18.203 1.318 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1146688909 69: 69: Generated 10 of the 10 non-bonded parameter combinations 69: 69: Generated 10 of the 10 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MimicTest.OneQuantumMol (10 ms) 69: [ RUN ] MimicTest.AllQuantumMol 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 21.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 69: 69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 80 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.018 0.009 199.5 69: (ns/day) (hour/ns) 69: Performance: 9.372 2.561 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1078001770 69: 69: Generated 10 of the 10 non-bonded parameter combinations 69: 69: Generated 10 of the 10 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MimicTest.AllQuantumMol (14 ms) 69: [ RUN ] MimicTest.TwoQuantumMol 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 21.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 69: 69: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.009 0.005 199.0 69: (ns/day) (hour/ns) 69: Performance: 18.204 1.318 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -145031362 69: 69: Generated 10 of the 10 non-bonded parameter combinations 69: 69: Generated 10 of the 10 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MimicTest.TwoQuantumMol (18 ms) 69: [ RUN ] MimicTest.BondCuts 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group rest is 66.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 69: NVE simulation: will use the initial temperature of 300.368 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.011 0.006 199.3 69: (ns/day) (hour/ns) 69: Performance: 15.310 1.568 69: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -943128577 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MimicTest.BondCuts (16 ms) 69: [----------] 4 tests from MimicTest (59 ms total) 69: 69: [----------] 2 tests from WithIntegrator/ImdTest 69: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 69: Generating 1-4 interactions: fudge = 1 69: 69: NOTE 1 [file glycine_vacuo.top, line 12]: 69: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 69: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 69: the time step of 2.0e-03 ps. 69: Maybe you forgot to change the constraints mdp option. 69: 69: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: IMD: Enabled. This simulation will accept incoming IMD connections. 69: IMD: Pulling from IMD remote is enabled (-imdpull). 69: IMD: Setting port for connection requests to 0. 69: IMD: Setting up incoming socket. 69: IMD: Listening for IMD connection on port 58865. 69: IMD: -imdwait not set, starting simulation. 69: starting mdrun 'Glycine' 69: 2 steps, 0.0 ps. 69: Setting the LD random seed to -1182210 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.034 0.017 199.5 69: (ns/day) (hour/ns) 69: Performance: 30.112 0.797 69: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (74 ms) 69: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 69: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 69: apply to steep. 69: 69: Generating 1-4 interactions: fudge = 1 69: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: IMD: Enabled. This simulation will accept incoming IMD connections. 69: IMD: Pulling from IMD remote is enabled (-imdpull). 69: IMD: Setting port for connection requests to 0. 69: IMD: Setting up incoming socket. 69: IMD: Listening for IMD connection on port 44187. 69: IMD: -imdwait not set, starting simulation. 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 2 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 3 steps. 69: Potential Energy = 1.1977061e+03 69: Maximum force = 1.7794875e+04 on atom 9 69: Norm of force = 7.8732895e+03 69: Setting the LD random seed to -1623204369 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (71 ms) 69: [----------] 2 tests from WithIntegrator/ImdTest (145 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 15 tests from 3 test suites ran. (340 ms total) 69: [ PASSED ] 15 tests. 69/96 Test #69: MdrunModulesTests ............................ Passed 0.43 sec test 70 Start 70: MdrunIOTests 70: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunIOTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 76 tests from 13 test suites. 70: [----------] Global test environment set-up. 70: [----------] 9 tests from GromppTest 70: [ RUN ] GromppTest.EmptyMdpFileWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Setting the LD random seed to -375393837 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 70: [ RUN ] GromppTest.SimulatedAnnealingWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Simulated annealing for group rest: Periodic, 4 timepoints 70: Time (ps) Temperature (K) 70: 0.0 298.0 70: 2.0 320.0 70: 4.0 320.0 70: 6.0 298.0 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Setting the LD random seed to -151585299 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] GromppTest.SimulatedAnnealingWorks (2 ms) 70: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Simulated annealing for group Methanol: Single, 3 timepoints 70: Time (ps) Temperature (K) 70: 0.0 298.0 70: 3.0 280.0 70: 6.0- 270.0 70: Simulated annealing for group SOL: Periodic, 4 timepoints 70: Time (ps) Temperature (K) 70: 0.0 298.0 70: 2.0 320.0 70: 4.0 320.0 70: 6.0 298.0 70: Number of degrees of freedom in T-Coupling group Methanol is 7.20 70: Number of degrees of freedom in T-Coupling group SOL is 4.80 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Setting the LD random seed to -1291917447 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 70: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 70: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) 70: [ RUN ] GromppTest.HandlesMaxwarn 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 70: The Berendsen thermostat does not generate the correct kinetic energy 70: distribution, and should not be used for new production simulations (in 70: our opinion). We would recommend the V-rescale thermostat. 70: 70: Number of degrees of freedom in T-Coupling group System is 12.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: 70: There was 1 WARNING 70: Setting the LD random seed to -68494349 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 70: [ RUN ] GromppTest.MaxwarnShouldBePositive 70: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 70: [ RUN ] GromppTest.ValidTransformationCoord 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Pull group 1 'SOL' has 3 atoms 70: Pull group 2 'Methanol' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 5 70: 2 3 2 0.613 nm 0.000 nm 70: 1 3 5 70: 2 3 2 0.613 nm 0.000 nm 70: 70: There were 3 NOTEs 70: Setting the LD random seed to -1124095069 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 70: [ RUN ] GromppTest.InvalidTransformationCoord 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Pull group 1 'SOL' has 3 atoms 70: Pull group 2 'Methanol' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 5 70: 2 3 2 0.613 nm 0.000 nm 70: 1 3 5 70: 2 3 2 Setting the LD random seed to -3244034 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: [ OK ] GromppTest.InvalidTransformationCoord (3 ms) 70: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 70: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) 70: [----------] 9 tests from GromppTest (18 ms total) 70: 70: [----------] 6 tests from MdrunTerminationTest 70: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -35803394 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.031 0.016 199.4 70: (ns/day) (hour/ns) 70: Performance: 16.505 1.454 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 4 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 2 70: Runtime for the run 0.002 ps 70: Run end step 2 70: Run end time 0.002 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 49 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.012 0.006 198.4 70: (ns/day) (hour/ns) 70: Performance: 43.781 0.548 70: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (38 ms) 70: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 1, rlist from 1.032 to 1 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 100 steps, 0.1 ps. 70: 70: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 70: Setting the LD random seed to 2004614623 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: 39 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.029 0.015 199.3 70: (ns/day) (hour/ns) 70: Performance: 11.692 2.053 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 102 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 100 70: Runtime for the run 0.1 ps 70: Run end step 100 70: Run end time 0.1 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 102 70: Runtime for the run 0.102 ps 70: Run end step 102 70: Run end time 0.102 ps 70: 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.543 0.272 200.0 70: (ns/day) (hour/ns) 70: Performance: 32.458 0.739 70: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (298 ms) 70: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to 1610149261 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.032 0.016 199.3 70: (ns/day) (hour/ns) 70: Performance: 16.190 1.482 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 4 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 2 70: Runtime for the run 0.002 ps 70: Run end step 2 70: Run end time 0.002 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 61 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.066 0.033 199.7 70: (ns/day) (hour/ns) 70: Performance: 7.792 3.080 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 6 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 6 70: Runtime for the run 0.006 ps 70: Run end step 6 70: Run end time 0.006 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 22 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.026 0.013 199.5 70: (ns/day) (hour/ns) 70: Performance: 19.558 1.227 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 8 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 6 70: Runtime for the run 0.006 ps 70: Run end step 6 70: Run end time 0.006 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 8 70: Runtime for the run 0.008 ps 70: Run end step 8 70: Run end time 0.008 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 22 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.026 0.013 199.5 70: (ns/day) (hour/ns) 70: Performance: 19.548 1.228 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: NOTE: 43 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.013 0.007 199.1 70: (ns/day) (hour/ns) 70: Performance: 12.883 1.863 70: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (148 ms) 70: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to 1583283818 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 20 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.030 0.015 199.2 70: (ns/day) (hour/ns) 70: Performance: 17.295 1.388 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 4 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 2 70: Runtime for the run 0.002 ps 70: Run end step 2 70: Run end time 0.002 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.041 0.021 199.6 70: (ns/day) (hour/ns) 70: Performance: 21.020 1.142 70: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (49 ms) 70: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -413139862 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.030 0.015 199.4 70: (ns/day) (hour/ns) 70: Performance: 17.273 1.389 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 4 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 2 70: Runtime for the run 0.002 ps 70: Run end step 2 70: Run end time 0.002 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (23 ms) 70: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There was 1 NOTE 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 2 steps, 0.0 ps. 70: Setting the LD random seed to -129 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.030 0.015 199.4 70: (ns/day) (hour/ns) 70: Performance: 17.104 1.403 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Setting nsteps to 4 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: Input file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 2 70: Runtime for the run 0.002 ps 70: Run end step 2 70: Run end time 0.002 ps 70: 70: 70: Output file: 70: Run start step 0 70: Run start time 0 ps 70: Step to be made during run 4 70: Runtime for the run 0.004 ps 70: Run end step 4 70: Run end time 0.004 ps 70: 70: 70: Writing final coordinates. 70: 70: NOTE: 34 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.017 0.008 199.1 70: (ns/day) (hour/ns) 70: Performance: 30.927 0.776 70: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (34 ms) 70: [----------] 6 tests from MdrunTerminationTest (592 ms total) 70: 70: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 70: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.137 0.068 199.8 70: (ns/day) (hour/ns) 70: Performance: 21.490 1.117 70: trr version: GMX_trn_file (single precision) 70: 70: 70: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (76 ms) 70: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 24 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.024 0.012 199.5 70: (ns/day) (hour/ns) 70: Performance: 120.796 0.199 70: 70: 70: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (18 ms) 70: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (94 ms total) 70: 70: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.086 0.043 199.7 70: (ns/day) (hour/ns) 70: Performance: 33.985 0.706 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.674 1.058 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.068 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.795 1.053 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (128 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 51 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.011 0.006 198.6 70: (ns/day) (hour/ns) 70: Performance: 256.606 0.094 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.035 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.391 1.072 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.035 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.351 1.074 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (91 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.139 0.070 199.9 70: (ns/day) (hour/ns) 70: Performance: 21.067 1.139 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.079 0.039 199.8 70: (ns/day) (hour/ns) 70: Performance: 19.713 1.217 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.076 0.038 199.7 70: (ns/day) (hour/ns) 70: Performance: 20.334 1.180 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (162 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.139 0.069 199.9 70: (ns/day) (hour/ns) 70: Performance: 21.137 1.135 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 51 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.312 0.156 200.0 70: (ns/day) (hour/ns) 70: Performance: 4.978 4.821 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 85 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.208 0.104 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.463 3.216 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (403 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.036 0.018 199.4 70: (ns/day) (hour/ns) 70: Performance: 81.269 0.295 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.8 70: (ns/day) (hour/ns) 70: Performance: 22.565 1.064 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.068 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.896 1.048 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (125 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.113 0.057 199.9 70: (ns/day) (hour/ns) 70: Performance: 25.988 0.923 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.045 0.023 199.5 70: (ns/day) (hour/ns) 70: Performance: 34.372 0.698 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.109 0.055 199.8 70: (ns/day) (hour/ns) 70: Performance: 14.189 1.691 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (150 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.056 0.028 199.6 70: (ns/day) (hour/ns) 70: Performance: 52.275 0.459 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 43 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.056 0.028 199.6 70: (ns/day) (hour/ns) 70: Performance: 27.655 0.868 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.128 0.064 199.8 70: (ns/day) (hour/ns) 70: Performance: 12.141 1.977 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (235 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 50 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.224 0.112 199.9 70: (ns/day) (hour/ns) 70: Performance: 13.102 1.832 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.096 0.048 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.192 1.482 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.024 0.012 199.2 70: (ns/day) (hour/ns) 70: Performance: 64.458 0.372 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (276 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.032 0.016 199.2 70: (ns/day) (hour/ns) 70: Performance: 90.996 0.264 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.083 0.042 199.8 70: (ns/day) (hour/ns) 70: Performance: 18.648 1.287 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.076 0.038 199.7 70: (ns/day) (hour/ns) 70: Performance: 20.521 1.170 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (190 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.135 0.068 199.8 70: (ns/day) (hour/ns) 70: Performance: 21.693 1.106 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.076 0.038 199.7 70: (ns/day) (hour/ns) 70: Performance: 20.526 1.169 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.076 0.038 199.7 70: (ns/day) (hour/ns) 70: Performance: 20.508 1.170 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (162 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.167 0.084 199.9 70: (ns/day) (hour/ns) 70: Performance: 17.542 1.368 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.095 0.047 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.424 1.461 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.082 0.041 199.7 70: (ns/day) (hour/ns) 70: Performance: 18.913 1.269 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (187 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 39 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.144 0.072 199.9 70: (ns/day) (hour/ns) 70: Performance: 20.344 1.180 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.088 0.044 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.588 1.365 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 75 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.096 0.048 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.125 1.488 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (264 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 35 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.320 0.160 199.9 70: (ns/day) (hour/ns) 70: Performance: 9.176 2.616 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.6 70: (ns/day) (hour/ns) 70: Performance: 24.223 0.991 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 34 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.328 0.164 199.9 70: (ns/day) (hour/ns) 70: Performance: 4.740 5.063 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (491 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.040 0.020 199.5 70: (ns/day) (hour/ns) 70: Performance: 73.109 0.328 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 45 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.232 0.116 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.699 3.582 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.7 70: (ns/day) (hour/ns) 70: Performance: 24.225 0.991 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (316 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.080 0.040 199.7 70: (ns/day) (hour/ns) 70: Performance: 36.667 0.655 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 24 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.200 0.100 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.771 3.088 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 25 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.195 0.098 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.954 3.017 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (373 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.056 0.028 199.6 70: (ns/day) (hour/ns) 70: Performance: 52.328 0.459 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.088 0.044 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.628 1.361 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.088 0.044 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.628 1.361 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (254 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.217 0.109 199.9 70: (ns/day) (hour/ns) 70: Performance: 13.521 1.775 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.140 0.070 199.8 70: (ns/day) (hour/ns) 70: Performance: 11.064 2.169 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.171 0.086 199.9 70: (ns/day) (hour/ns) 70: Performance: 9.077 2.644 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (334 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.036 0.018 199.3 70: (ns/day) (hour/ns) 70: Performance: 81.403 0.295 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 20 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.028 0.014 199.1 70: (ns/day) (hour/ns) 70: Performance: 55.396 0.433 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.225 0.113 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.901 3.478 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (210 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.453 0.227 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.484 3.702 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.136 0.068 199.8 70: (ns/day) (hour/ns) 70: Performance: 11.427 2.100 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.236 0.118 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.594 3.640 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (580 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: NVE simulation: will use the initial temperature of 456.887 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.122 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 24.094 0.996 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.214 0.107 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.278 3.298 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.244 0.122 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.367 3.769 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (344 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.170 0.085 199.9 70: (ns/day) (hour/ns) 70: Performance: 17.283 1.389 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.024 0.012 199.0 70: (ns/day) (hour/ns) 70: Performance: 64.735 0.371 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.039 199.7 70: (ns/day) (hour/ns) 70: Performance: 19.865 1.208 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (321 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.339 0.169 199.9 70: (ns/day) (hour/ns) 70: Performance: 8.667 2.769 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.166 0.083 199.9 70: (ns/day) (hour/ns) 70: Performance: 9.386 2.557 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.180 0.090 199.9 70: (ns/day) (hour/ns) 70: Performance: 8.625 2.783 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (467 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.016 0.008 198.5 70: (ns/day) (hour/ns) 70: Performance: 182.861 0.131 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.297 0.149 199.9 70: (ns/day) (hour/ns) 70: Performance: 5.226 4.592 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.322 0.161 199.9 70: (ns/day) (hour/ns) 70: Performance: 4.828 4.971 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (402 ms) 70: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: There are 9 non-linear virtual site constructions. Their contribution to 70: the energy error is approximated. In most cases this does not affect the 70: error significantly. 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.159 0.079 199.8 70: (ns/day) (hour/ns) 70: Performance: 18.478 1.299 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.084 0.042 199.7 70: (ns/day) (hour/ns) 70: Performance: 18.415 1.303 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 70: 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine dipeptide in vacuo' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.189 0.095 199.9 70: (ns/day) (hour/ns) 70: Performance: 8.219 2.920 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (308 ms) 70: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (6784 ms total) 70: 70: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.189 0.095 199.9 70: (ns/day) (hour/ns) 70: Performance: 15.498 1.549 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.063 0.032 199.7 70: (ns/day) (hour/ns) 70: Performance: 24.549 0.978 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.5 70: (ns/day) (hour/ns) 70: Performance: 24.196 0.992 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (233 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.022 0.011 198.6 70: (ns/day) (hour/ns) 70: Performance: 132.832 0.181 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.100 0.050 199.8 70: (ns/day) (hour/ns) 70: Performance: 15.466 1.552 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.100 0.050 199.8 70: (ns/day) (hour/ns) 70: Performance: 15.546 1.544 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (184 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.039 199.8 70: (ns/day) (hour/ns) 70: Performance: 37.534 0.639 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 73 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.088 0.044 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.644 1.360 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.124 0.062 199.8 70: (ns/day) (hour/ns) 70: Performance: 12.561 1.911 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (177 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 294.908 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 47 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.122 0.061 199.9 70: (ns/day) (hour/ns) 70: Performance: 24.089 0.996 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.130 0.065 199.9 70: (ns/day) (hour/ns) 70: Performance: 11.970 2.005 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.123 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 12.672 1.894 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (218 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.192 0.096 199.9 70: (ns/day) (hour/ns) 70: Performance: 15.268 1.572 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.103 0.051 199.8 70: (ns/day) (hour/ns) 70: Performance: 15.131 1.586 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.101 0.051 199.7 70: (ns/day) (hour/ns) 70: Performance: 15.391 1.559 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (252 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.122 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 23.980 1.001 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.096 0.048 199.7 70: (ns/day) (hour/ns) 70: Performance: 16.197 1.482 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.016 0.008 198.3 70: (ns/day) (hour/ns) 70: Performance: 96.835 0.248 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (270 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.172 0.086 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.091 1.404 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.176 0.088 199.8 70: (ns/day) (hour/ns) 70: Performance: 8.830 2.718 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 47 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.218 0.109 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.140 3.361 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (508 ms) 70: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.122 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 23.953 1.002 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.125 0.063 199.8 70: (ns/day) (hour/ns) 70: Performance: 12.400 1.935 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.091 0.046 199.7 70: (ns/day) (hour/ns) 70: Performance: 16.993 1.412 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (284 ms) 70: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2131 ms total) 70: 70: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.122 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 24.105 0.996 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.068 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.770 1.054 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.068 0.034 199.8 70: (ns/day) (hour/ns) 70: Performance: 22.791 1.053 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (145 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.071 0.036 199.6 70: (ns/day) (hour/ns) 70: Performance: 41.302 0.581 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.7 70: (ns/day) (hour/ns) 70: Performance: 24.149 0.994 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.089 0.045 199.7 70: (ns/day) (hour/ns) 70: Performance: 17.385 1.380 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (149 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.096 0.048 199.7 70: (ns/day) (hour/ns) 70: Performance: 30.628 0.784 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 47 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.240 0.120 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.475 3.707 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 32 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.105 0.052 199.8 70: (ns/day) (hour/ns) 70: Performance: 14.818 1.620 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (320 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.113 0.056 199.8 70: (ns/day) (hour/ns) 70: Performance: 26.060 0.921 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.7 70: (ns/day) (hour/ns) 70: Performance: 24.308 0.987 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.7 70: (ns/day) (hour/ns) 70: Performance: 24.227 0.991 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (137 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.139 0.069 199.9 70: (ns/day) (hour/ns) 70: Performance: 21.152 1.135 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.039 199.8 70: (ns/day) (hour/ns) 70: Performance: 19.848 1.209 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.077 0.038 199.7 70: (ns/day) (hour/ns) 70: Performance: 20.204 1.188 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (161 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.130 0.065 199.9 70: (ns/day) (hour/ns) 70: Performance: 22.578 1.063 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.074 0.037 199.8 70: (ns/day) (hour/ns) 70: Performance: 20.947 1.146 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.208 0.104 199.9 70: (ns/day) (hour/ns) 70: Performance: 7.463 3.216 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (220 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.048 0.024 199.7 70: (ns/day) (hour/ns) 70: Performance: 60.634 0.396 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.096 0.048 199.9 70: (ns/day) (hour/ns) 70: Performance: 16.180 1.483 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.085 0.043 199.7 70: (ns/day) (hour/ns) 70: Performance: 18.288 1.312 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (181 ms) 70: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.147 0.074 199.9 70: (ns/day) (hour/ns) 70: Performance: 19.940 1.204 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 29 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.020 0.010 199.1 70: (ns/day) (hour/ns) 70: Performance: 78.191 0.307 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 70: 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.081 0.041 199.7 70: (ns/day) (hour/ns) 70: Performance: 19.124 1.255 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (141 ms) 70: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1457 ms total) 70: 70: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 70: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.121 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 24.199 0.992 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.007 0.003 196.6 70: (ns/day) (hour/ns) 70: Performance: 228.012 0.105 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.665 1.059 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (114 ms) 70: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 68.810 K for 70: determining the Verlet buffer size 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.139 0.069 199.9 70: (ns/day) (hour/ns) 70: Performance: 21.135 1.136 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 28 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.021 0.011 199.3 70: (ns/day) (hour/ns) 70: Performance: 73.985 0.324 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.076 0.038 199.6 70: (ns/day) (hour/ns) 70: Performance: 20.383 1.177 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (131 ms) 70: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (246 ms total) 70: 70: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.121 0.061 199.8 70: (ns/day) (hour/ns) 70: Performance: 24.213 0.991 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.050 0.025 199.5 70: (ns/day) (hour/ns) 70: Performance: 30.780 0.780 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.569 1.063 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (137 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.094 0.047 199.8 70: (ns/day) (hour/ns) 70: Performance: 31.276 0.767 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.071 0.036 199.7 70: (ns/day) (hour/ns) 70: Performance: 21.816 1.100 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.071 0.036 199.7 70: (ns/day) (hour/ns) 70: Performance: 21.839 1.099 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (135 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 42 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.014 0.007 198.2 70: (ns/day) (hour/ns) 70: Performance: 210.763 0.114 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.035 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.427 1.070 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 17 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.7 70: (ns/day) (hour/ns) 70: Performance: 22.635 1.060 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (92 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 70: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 70: 1 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 30 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.020 0.010 198.8 70: (ns/day) (hour/ns) 70: Performance: 149.203 0.161 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.124 0.062 199.8 70: (ns/day) (hour/ns) 70: Performance: 12.497 1.920 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 44 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.256 0.128 199.9 70: (ns/day) (hour/ns) 70: Performance: 6.073 3.952 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (238 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 62 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.360 0.180 200.0 70: (ns/day) (hour/ns) 70: Performance: 8.152 2.944 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 71 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.080 0.040 199.8 70: (ns/day) (hour/ns) 70: Performance: 19.497 1.231 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.137 0.068 199.8 70: (ns/day) (hour/ns) 70: Performance: 11.362 2.112 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (366 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 14 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.232 0.116 199.9 70: (ns/day) (hour/ns) 70: Performance: 12.672 1.894 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.089 0.045 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.391 1.380 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.087 0.043 199.7 70: (ns/day) (hour/ns) 70: Performance: 17.896 1.341 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (229 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 70: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 70: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 11 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.160 0.080 199.9 70: (ns/day) (hour/ns) 70: Performance: 18.361 1.307 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.090 0.045 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.232 1.393 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.088 0.044 199.6 70: (ns/day) (hour/ns) 70: Performance: 17.722 1.354 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (184 ms) 70: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1383 ms total) 70: 70: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 70: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: MTTK coupling is deprecated and will soon be removed 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: MTTK coupling is deprecated and will soon be removed 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps. 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.133 0.066 199.9 70: (ns/day) (hour/ns) 70: Performance: 22.118 1.085 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.069 0.034 199.8 70: (ns/day) (hour/ns) 70: Performance: 22.633 1.060 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.143 0.072 199.8 70: (ns/day) (hour/ns) 70: Performance: 10.851 2.212 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (188 ms) 70: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (188 ms total) 70: 70: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 70: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.140 0.070 199.8 70: (ns/day) (hour/ns) 70: Performance: 20.991 1.143 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.039 199.7 70: (ns/day) (hour/ns) 70: Performance: 19.816 1.211 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 15 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.039 199.7 70: (ns/day) (hour/ns) 70: Performance: 19.903 1.206 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (169 ms) 70: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There were 3 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group System is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 2573.591 K for 70: determining the Verlet buffer size 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps. 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 24 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.049 0.025 199.5 70: (ns/day) (hour/ns) 70: Performance: 59.828 0.401 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.090 0.045 199.8 70: (ns/day) (hour/ns) 70: Performance: 17.247 1.392 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 85 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.104 0.052 199.7 70: (ns/day) (hour/ns) 70: Performance: 14.918 1.609 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (138 ms) 70: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (308 ms total) 70: 70: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 70: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: Setting the AWH bias MC random seed to 2143285183 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'C_&_r_1' has 1 atoms 70: Pull group 2 'N_&_r_2' has 1 atoms 70: Pull group 3 'CA' has 1 atoms 70: Pull group 4 'C_&_r_2' has 1 atoms 70: Pull group 5 'N_&_r_3' has 1 atoms 70: Number of degrees of freedom in T-Coupling group System is 51.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 1 0 70: 2 1 0 179.098 deg 0.000 deg 70: 2 1 0 70: 3 1 0 158.667 deg 0.000 deg 70: 70: There were 3 NOTEs 70: Setting the AWH bias MC random seed to -3318593 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'C_&_r_1' has 1 atoms 70: Pull group 2 'N_&_r_2' has 1 atoms 70: Pull group 3 'CA' has 1 atoms 70: Pull group 4 'C_&_r_2' has 1 atoms 70: Pull group 5 'N_&_r_3' has 1 atoms 70: Number of degrees of freedom in T-Coupling group System is 51.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 1 0 70: 2 1 0 179.098 deg 0.000 deg 70: 2 1 0 70: 3 1 0 158.667 deg 0.000 deg 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.008 0.004 195.4 70: (ns/day) (hour/ns) 70: Performance: 359.680 0.067 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.016 0.008 197.6 70: (ns/day) (hour/ns) 70: Performance: 94.866 0.253 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 36 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.312 0.156 199.9 70: (ns/day) (hour/ns) 70: Performance: 4.985 4.815 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (331 ms) 70: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 70: Setting the AWH bias MC random seed to -673187841 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'C_&_r_1' has 1 atoms 70: Pull group 2 'N_&_r_2' has 1 atoms 70: Pull group 3 'CA' has 1 atoms 70: Pull group 4 'C_&_r_2' has 1 atoms 70: Pull group 5 'N_&_r_3' has 1 atoms 70: Number of degrees of freedom in T-Coupling group System is 51.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 1 0 70: 2 1 0 179.098 deg 0.000 deg 70: 2 1 0 70: 3 1 0 158.667 deg 0.000 deg 70: 70: There were 3 NOTEs 70: Setting the AWH bias MC random seed to 1925124066 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'C_&_r_1' has 1 atoms 70: Pull group 2 'N_&_r_2' has 1 atoms 70: Pull group 3 'CA' has 1 atoms 70: Pull group 4 'C_&_r_2' has 1 atoms 70: Pull group 5 'N_&_r_3' has 1 atoms 70: Number of degrees of freedom in T-Coupling group System is 51.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 1 0 70: 2 1 0 179.098 deg 0.000 deg 70: 2 1 0 70: 3 1 0 158.667 deg 0.000 deg 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 16 steps, 0.0 ps. 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.041 0.021 199.0 70: (ns/day) (hour/ns) 70: Performance: 71.264 0.337 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.119 0.059 199.7 70: (ns/day) (hour/ns) 70: Performance: 13.087 1.834 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 27 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.021 0.011 198.3 70: (ns/day) (hour/ns) 70: Performance: 72.484 0.331 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (202 ms) 70: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (534 ms total) 70: 70: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 70: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 79.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps. 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Generated 2485 of the 2485 non-bonded parameter combinations 70: 70: Generated 2485 of the 2485 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'nonanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 12 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.165 0.082 199.9 70: (ns/day) (hour/ns) 70: Performance: 17.848 1.345 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.137 0.068 199.9 70: (ns/day) (hour/ns) 70: Performance: 11.374 2.110 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun '30 atom system in water' 70: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.131 0.065 199.7 70: (ns/day) (hour/ns) 70: Performance: 11.896 2.017 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (258 ms) 70: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (258 ms total) 70: 70: [----------] 3 tests from Checking/InitialConstraintsTest 70: [ RUN ] Checking/InitialConstraintsTest.Works/0 70: Number of degrees of freedom in T-Coupling group rest is 11.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 1141.954 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 1 steps, 0.0 ps. 70: Setting the LD random seed to -35663057 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 35 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.015 0.007 198.4 70: (ns/day) (hour/ns) 70: Performance: 23.357 1.028 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (18 ms) 70: [ RUN ] Checking/InitialConstraintsTest.Works/1 70: Number of degrees of freedom in T-Coupling group rest is 11.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 1141.954 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 1 steps, 0.0 ps. 70: Setting the LD random seed to -1613239349 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.038 0.019 199.6 70: (ns/day) (hour/ns) 70: Performance: 9.149 2.623 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (26 ms) 70: [ RUN ] Checking/InitialConstraintsTest.Works/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 70: Integrator method md-vv-avek is implemented primarily for validation 70: purposes; for molecular dynamics, you should probably be using md or 70: md-vv 70: 70: Number of degrees of freedom in T-Coupling group rest is 11.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 1141.954 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 1 steps, 0.0 ps. 70: Setting the LD random seed to -840319044 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: turning H bonds into constraints... 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 70: 70: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: Writing final coordinates. 70: 70: NOTE: 13 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.038 0.019 199.4 70: (ns/day) (hour/ns) 70: Performance: 8.984 2.671 70: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (31 ms) 70: [----------] 3 tests from Checking/InitialConstraintsTest (75 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 76 tests from 13 test suites ran. (14123 ms total) 70: [ PASSED ] 76 tests. 70/96 Test #70: MdrunIOTests ................................. Passed 14.24 sec test 71 Start 71: MdrunTestsOneRank 71: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 29 tests from 8 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from CompelTest 71: [ RUN ] CompelTest.SwapCanRun 71: Setting the LD random seed to 1912339930 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein' 71: 71: turning all bonds into constraints... 71: 71: Excluding 3 bonded neighbours molecule type 'OCT' 71: 71: turning all bonds into constraints... 71: 71: Excluding 1 bonded neighbours molecule type 'NA' 71: 71: turning all bonds into constraints... 71: 71: Excluding 1 bonded neighbours molecule type 'CL' 71: 71: turning all bonds into constraints... 71: 71: Excluding 3 bonded neighbours molecule type 'Protein' 71: 71: Excluding 3 bonded neighbours molecule type 'OCT' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning all bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 71: Split0 group 'Ch0' contains 83 atoms. 71: Split1 group 'Ch1' contains 83 atoms. 71: Solvent group 'SOL' contains 11931 atoms. 71: Swap group 'NA+' contains 19 atoms. 71: Swap group 'CL-' contains 19 atoms. 71: Number of degrees of freedom in T-Coupling group System is 27869.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 71: Removing center of mass motion in the presence of position restraints 71: might cause artifacts. When you are using position restraints to 71: equilibrate a macro-molecule, the artifacts are usually negligible. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 1 Mb of data 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Update groups can not be used for this system because there are three or more consecutively coupled constraints 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: SWAP: Determining initial numbers of ions per compartment. 71: SWAP: Setting pointers for checkpoint writing 71: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 71: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 71: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 71: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 71: starting mdrun 'Channel_coco in octane membrane' 71: 2 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.448 0.224 199.9 71: (ns/day) (hour/ns) 71: Performance: 5.780 4.152 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 71: 71: Update groups can not be used for this system because there are three or more consecutively coupled constraints 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: SWAP: Setting pointers for checkpoint writing 71: SWAP: Copying channel fluxes from checkpoint file data 71: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 71: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 71: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 71: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 71: starting mdrun 'Channel_coco in octane membrane' 71: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 71: 71: Writing final coordinates. 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.241 0.121 199.9 71: (ns/day) (hour/ns) 71: Performance: 10.740 2.235 71: [ OK ] CompelTest.SwapCanRun (610 ms) 71: [----------] 1 test from CompelTest (610 ms total) 71: 71: [----------] 6 tests from BondedInteractionsTest 71: [ RUN ] BondedInteractionsTest.NormalBondWorks 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 2 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: Setting the LD random seed to -202377217 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 52 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.011 0.006 199.3 71: (ns/day) (hour/ns) 71: Performance: 15.626 1.536 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 2 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: [ OK ] BondedInteractionsTest.NormalBondWorks (10 ms) 71: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 71: Setting the LD random seed to -1093222401 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 52 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.011 0.006 199.3 71: (ns/day) (hour/ns) 71: Performance: 15.643 1.534 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 4 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: [ OK ] BondedInteractionsTest.TabulatedBondWorks (11 ms) 71: [ RUN ] BondedInteractionsTest.NormalAngleWorks 71: Setting the LD random seed to 1844441405 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 53 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.011 0.006 199.4 71: (ns/day) (hour/ns) 71: Performance: 15.616 1.537 71: [ OK ] BondedInteractionsTest.NormalAngleWorks (10 ms) 71: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 4 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: Setting the LD random seed to 2147434495 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.000 0.000 184.8 71: (ns/day) (hour/ns) 71: Performance: 531.361 0.045 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 4 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (3 ms) 71: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 71: Setting the LD random seed to -407127585 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 19 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.000 0.000 185.0 71: (ns/day) (hour/ns) 71: Performance: 502.618 0.048 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 71: In moleculetype 'butane' 4 atoms are not bound by a potential or 71: constraint to any other atom in the same moleculetype. Although 71: technically this might not cause issues in a simulation, this often means 71: that the user forgot to add a bond/potential/constraint or put multiple 71: molecules in the same moleculetype definition by mistake. Run with -v to 71: get information for each atom. 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: [ OK ] BondedInteractionsTest.NormalDihedralWorks (3 ms) 71: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 71: Setting the LD random seed to -5254178 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'butane' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 71: 71: Reading frames from gro file 'A single butane', 4 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 19 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.000 0.000 187.1 71: (ns/day) (hour/ns) 71: Performance: 485.775 0.049 71: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (4 ms) 71: [----------] 6 tests from BondedInteractionsTest (45 ms total) 71: 71: [----------] 2 tests from BoxDeformationTest 71: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (10) 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Number of degrees of freedom in T-Coupling group rest is 33.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: Setting the LD random seed to -285750625 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Setting gen_seed to -6308356 71: 71: Velocities were taken from a Maxwell distribution at 0 K 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 0 steps, 0.0 ps. 71: 71: NOTE: 24 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.000 0.000 163.2 71: (ns/day) (hour/ns) 71: Performance: 1170.882 0.020 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (10) 71: 71: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (9 ms) 71: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 71: Setting the LD random seed to 2006973422 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 71: Number of degrees of freedom in T-Coupling group rest is 1293.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: There were 2 NOTEs 71: 71: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 71: 71: Estimate for the relative computational load of the PME mesh part: 0.23 71: 71: This run will generate roughly 0 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.209 0.104 199.9 71: (ns/day) (hour/ns) 71: Performance: 34.725 0.691 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 71: You have set rlist larger than the interaction cut-off, but you also have 71: verlet-buffer-tolerance > 0. Will set rlist using 71: verlet-buffer-tolerance. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (10) 71: 71: [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1410 ms) 71: [----------] 2 tests from BoxDeformationTest (1420 ms total) 71: 71: [----------] 1 test from PositionRestraintCommTest 71: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 71: Setting the LD random seed to -141312242 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein' 71: 71: Excluding 3 bonded neighbours molecule type 'OCT' 71: 71: Excluding 1 bonded neighbours molecule type 'NA' 71: 71: Excluding 1 bonded neighbours molecule type 'CL' 71: 71: Excluding 3 bonded neighbours molecule type 'Protein' 71: 71: Excluding 3 bonded neighbours molecule type 'OCT' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 71: 13489 atoms are not part of any of the VCM groups 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 71: 13489 atoms are not part of any center of mass motion removal group. 71: This may lead to artifacts. 71: In most cases one should use one group for the whole system. 71: 71: Number of degrees of freedom in T-Coupling group System is 29527.73 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 71: Removing center of mass motion in the presence of position restraints 71: might cause artifacts. When you are using position restraints to 71: equilibrate a macro-molecule, the artifacts are usually negligible. 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: Chain0: 2.207 2.168 7.330 71: Chain1: 2.228 2.186 2.401 71: Chain0: 2.207 2.168 7.330 71: Chain1: 2.228 2.186 2.401 71: 71: This run will generate roughly 1 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Channel_coco in octane membrane' 71: 10 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 10 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.452 0.226 199.9 71: (ns/day) (hour/ns) 71: Performance: 8.406 2.855 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (436 ms) 71: [----------] 1 test from PositionRestraintCommTest (436 ms total) 71: 71: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 71: Setting the LD random seed to -1090781185 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 71: 71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 71: 71: Estimate for the relative computational load of the PME mesh part: 0.95 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE 2 [file ala.top, line 256]: 71: For energy conservation with LINCS, lincs_iter should be 2 or larger. 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 54.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'UNNAMED in water' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 14 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.102 0.051 199.8 71: (ns/day) (hour/ns) 71: Performance: 8.456 2.838 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Setting the LD random seed to 2113332059 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: NOTE 2 [file ala.top, line 256]: 71: For energy conservation with LINCS, lincs_iter should be 2 or larger. 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 54.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 71: 71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 71: 71: Estimate for the relative computational load of the PME mesh part: 0.95 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'UNNAMED in water' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 15 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.092 0.046 199.8 71: (ns/day) (hour/ns) 71: Performance: 9.340 2.570 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 71: 71: 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (23908 ms) 71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Setting the LD random seed to -340267195 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: NOTE 2 [file ala.top, line 256]: 71: For energy conservation with LINCS, lincs_iter should be 2 or larger. 71: 71: 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 71: Number of degrees of freedom in T-Coupling group rest is 54.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 71: 71: Estimate for the relative computational load of the PME mesh part: 0.95 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: This run will generate roughly 0 Mb of data 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'UNNAMED in water' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 14 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.102 0.051 199.7 71: (ns/day) (hour/ns) 71: Performance: 8.422 2.850 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Setting the LD random seed to 2147433850 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 71: 71: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 71: 71: Estimate for the relative computational load of the PME mesh part: 0.95 71: 71: This run will generate roughly 0 Mb of data 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file ala.top, line 256]: 71: For energy conservation with LINCS, lincs_iter should be 2 or larger. 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 54.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 71: Can not increase nstlist because an NVE ensemble is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'UNNAMED in water' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 16 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.091 0.046 199.8 71: (ns/day) (hour/ns) 71: Performance: 9.436 2.543 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 71: 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (148 ms) 71: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24057 ms total) 71: 71: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 71: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Setting the LD random seed to -1212417095 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 71: Pull group 1 'FirstWaterMolecule' has 3 atoms 71: Pull group 2 'SecondWaterMolecule' has 3 atoms 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: Pull group natoms pbc atom distance at start reference at t=0 71: 1 3 2 71: 2 3 5 1.112 nm 1.000 nm 71: 71: This run will generate roughly 0 Mb of data 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 14 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.043 0.021 199.4 71: (ns/day) (hour/ns) 71: Performance: 20.248 1.185 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: Setting the LD random seed to -111443969 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 71: Pull group 1 'FirstWaterMolecule' has 3 atoms 71: Pull group 2 'SecondWaterMolecule' has 3 atoms 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: Pull group natoms pbc atom distance at start reference at t=0 71: 1 3 2 71: 2 3 5 1.112 nm 1.000 nm 71: 71: This run will generate roughly 0 Mb of data 71: 71: There was 1 NOTE 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 71: Can not increase nstlist because an NVE ensemble is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 4 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.116 0.058 199.7 71: (ns/day) (hour/ns) 71: Performance: 7.462 3.216 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 71: 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (100 ms) 71: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (100 ms total) 71: 71: [----------] 12 tests from FreezeWorks/FreezeGroupTest 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: NVE simulation: will use the initial temperature of 246.451 K for 71: determining the Verlet buffer size 71: 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: This run will generate roughly 0 Mb of data 71: 71: There were 5 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.184 0.092 199.8 71: (ns/day) (hour/ns) 71: Performance: 8.445 2.842 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (184 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: Generating 1-4 interactions: fudge = 0.5 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: NVE simulation: will use the initial temperature of 246.451 K for 71: determining the Verlet buffer size 71: 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: This run will generate roughly 0 Mb of data 71: 71: There were 5 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.014 0.007 198.0 71: (ns/day) (hour/ns) 71: Performance: 111.079 0.216 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (51 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: NVE simulation: will use the initial temperature of 246.451 K for 71: determining the Verlet buffer size 71: 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: This run will generate roughly 0 Mb of data 71: 71: There were 5 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.091 0.045 199.8 71: (ns/day) (hour/ns) 71: Performance: 17.109 1.403 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (60 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 71: Generating 1-4 interactions: fudge = 0.5 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: NVE simulation: will use the initial temperature of 246.451 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.086 0.043 199.8 71: (ns/day) (hour/ns) 71: Performance: 18.053 1.329 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (57 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: NVE simulation: will use the initial temperature of 246.451 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: 71: There was 1 WARNING 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.071 0.036 199.6 71: (ns/day) (hour/ns) 71: Performance: 21.725 1.105 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (55 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 71: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 71: Parrinello-Rahman is not implemented in md-vv. 71: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.072 0.036 199.6 71: (ns/day) (hour/ns) 71: Performance: 21.566 1.113 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (107 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.104 0.052 199.7 71: (ns/day) (hour/ns) 71: Performance: 14.932 1.607 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (79 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.108 0.054 199.8 71: (ns/day) (hour/ns) 71: Performance: 14.370 1.670 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (70 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.087 0.043 199.8 71: (ns/day) (hour/ns) 71: Performance: 17.951 1.337 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (71 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.090 0.045 199.7 71: (ns/day) (hour/ns) 71: Performance: 17.342 1.384 71: 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (73 ms) 71: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 71: There are 5 atoms that are fully frozen and part of COMM removal 71: group(s), removing these atoms from the COMM removal group(s) 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 71: There are 3 atoms that are frozen along less then 3 dimensions and part 71: of COMM removal group(s), due to limitations in the code these still 71: contribute to the mass of the COM along frozen dimensions and therefore 71: the COMM correction will be too small. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine-dipeptide' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.087 0.044 199.8 71: (ns/day) (hour/ns) 71: Performance: 17.834 1.346 71: 71: 71: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (72 ms) 71: [----------] 12 tests from FreezeWorks/FreezeGroupTest (892 ms total) 71: 71: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: Net Acceleration in X direction, will not be corrected 71: Net Acceleration in Y direction, will not be corrected 71: Net Acceleration in Z direction, will not be corrected 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Setting gen_seed to -20971529 71: 71: Velocities were taken from a Maxwell distribution at 0 K 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 17 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.068 0.034 199.7 71: (ns/day) (hour/ns) 71: Performance: 45.423 0.528 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 71: Net Acceleration in X direction, will not be corrected 71: Net Acceleration in Y direction, will not be corrected 71: Net Acceleration in Z direction, will not be corrected 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: Can not increase nstlist because verlet-buffer-tolerance is not set or used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (41 ms) 71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Setting gen_seed to -1073742915 71: 71: Velocities were taken from a Maxwell distribution at 0 K 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 17 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.069 0.034 199.7 71: (ns/day) (hour/ns) 71: Performance: 45.247 0.530 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: Net Acceleration in X direction, will not be corrected 71: Net Acceleration in Y direction, will not be corrected 71: Net Acceleration in Z direction, will not be corrected 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (41 ms) 71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Setting gen_seed to 2090852287 71: 71: Velocities were taken from a Maxwell distribution at 0 K 71: 71: This run will generate roughly 0 Mb of data 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.090 0.045 199.8 71: (ns/day) (hour/ns) 71: Performance: 34.675 0.692 71: 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 71: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 71: < 0 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 71: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 71: Net Acceleration in X direction, will not be corrected 71: Net Acceleration in Y direction, will not be corrected 71: Net Acceleration in Z direction, will not be corrected 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (51 ms) 71: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Setting gen_seed to -413928593 71: 71: Velocities were taken from a Maxwell distribution at 0 K 71: 71: This run will generate roughly 0 Mb of data 71: Can not increase nstlist because verlet-buffer-tolerance is not set or used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 8 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.089 0.045 199.8 71: (ns/day) (hour/ns) 71: Performance: 34.846 0.689 71: 71: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (51 ms) 71: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (185 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 29 tests from 8 test suites ran. (27782 ms total) 71: [ PASSED ] 28 tests. 71: [ SKIPPED ] 1 test, listed below: 71: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 71/96 Test #71: MdrunTestsOneRank ............................ Passed 27.94 sec test 72 Start 72: MdrunTestsTwoRanks 72: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 29 tests from 8 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from CompelTest 72: [ RUN ] CompelTest.SwapCanRun 72: Setting the LD random seed to -151535873 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein' 72: 72: turning all bonds into constraints... 72: 72: Excluding 3 bonded neighbours molecule type 'OCT' 72: 72: turning all bonds into constraints... 72: 72: Excluding 1 bonded neighbours molecule type 'NA' 72: 72: turning all bonds into constraints... 72: 72: Excluding 1 bonded neighbours molecule type 'CL' 72: 72: turning all bonds into constraints... 72: 72: Excluding 3 bonded neighbours molecule type 'Protein' 72: 72: Excluding 3 bonded neighbours molecule type 'OCT' 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 72: Split0 group 'Ch0' contains 83 atoms. 72: Split1 group 'Ch1' contains 83 atoms. 72: Solvent group 'SOL' contains 11931 atoms. 72: Swap group 'NA+' contains 19 atoms. 72: Swap group 'CL-' contains 19 atoms. 72: Number of degrees of freedom in T-Coupling group System is 27869.00 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 72: Removing center of mass motion in the presence of position restraints 72: might cause artifacts. When you are using position restraints to 72: equilibrate a macro-molecule, the artifacts are usually negligible. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 72: 72: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 1 Mb of data 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Update groups can not be used for this system because there are three or more consecutively coupled constraints 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: SWAP: Determining initial numbers of ions per compartment. 72: SWAP: Setting pointers for checkpoint writing 72: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 72: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 72: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 72: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 72: starting mdrun 'Channel_coco in octane membrane' 72: 2 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 1.8%. 72: The balanceable part of the MD step is 9%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.2%. 72: 72: 72: NOTE: 28 % of the run time was spent in domain decomposition, 72: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 1.142 0.285 399.9 72: (ns/day) (hour/ns) 72: Performance: 4.540 5.287 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 72: 72: Update groups can not be used for this system because there are three or more consecutively coupled constraints 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: SWAP: Setting pointers for checkpoint writing 72: SWAP: Copying channel fluxes from checkpoint file data 72: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 72: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 72: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 72: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 72: starting mdrun 'Channel_coco in octane membrane' 72: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 72: 72: Writing final coordinates. 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.394 0.099 399.6 72: (ns/day) (hour/ns) 72: Performance: 13.151 1.825 72: [ OK ] CompelTest.SwapCanRun (828 ms) 72: [----------] 1 test from CompelTest (828 ms total) 72: 72: [----------] 6 tests from BondedInteractionsTest 72: [ RUN ] BondedInteractionsTest.NormalBondWorks 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: 72: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 2 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: Setting the LD random seed to -47716555 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: This run will generate roughly 0 Mb of data 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 70 % of the run time was spent in domain decomposition, 72: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.117 0.029 399.6 72: (ns/day) (hour/ns) 72: Performance: 2.946 8.145 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: 72: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 2 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: [ OK ] BondedInteractionsTest.NormalBondWorks (40 ms) 72: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 72: Setting the LD random seed to -7688290 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: This run will generate roughly 0 Mb of data 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 49 % of the run time was spent in domain decomposition, 72: 15 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: NOTE: 28 % of the run time was spent communicating energies, 72: you might want to increase some nst* mdp options 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.067 0.017 399.3 72: (ns/day) (hour/ns) 72: Performance: 5.111 4.696 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: 72: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: [ OK ] BondedInteractionsTest.TabulatedBondWorks (31 ms) 72: [ RUN ] BondedInteractionsTest.NormalAngleWorks 72: Setting the LD random seed to -1232273 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: This run will generate roughly 0 Mb of data 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 47 % of the run time was spent in domain decomposition, 72: 35 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.058 0.015 399.3 72: (ns/day) (hour/ns) 72: Performance: 5.913 4.059 72: [ OK ] BondedInteractionsTest.NormalAngleWorks (41 ms) 72: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Setting the LD random seed to -2310307 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 47 % of the run time was spent in domain decomposition, 72: 35 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.058 0.015 399.3 72: (ns/day) (hour/ns) 72: Performance: 5.918 4.055 72: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (28 ms) 72: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Setting the LD random seed to 2013265595 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 45 % of the run time was spent in domain decomposition, 72: 33 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.061 0.015 399.3 72: (ns/day) (hour/ns) 72: Performance: 5.625 4.266 72: [ OK ] BondedInteractionsTest.NormalDihedralWorks (27 ms) 72: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Setting the LD random seed to 2079293405 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 72: 72: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/butane1.gro' 72: 72: Reading frames from gro file 'A single butane', 4 atoms. 72: Reading frame 0 time 0.000 Last frame 0 time 0.000 72: 72: NOTE: 45 % of the run time was spent in domain decomposition, 72: 33 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.061 0.015 399.4 72: (ns/day) (hour/ns) 72: Performance: 5.627 4.265 72: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (28 ms) 72: [----------] 6 tests from BondedInteractionsTest (199 ms total) 72: 72: [----------] 2 tests from BoxDeformationTest 72: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (10) 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Setting the LD random seed to -33639425 72: 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Setting gen_seed to -1891664898 72: 72: Velocities were taken from a Maxwell distribution at 0 K 72: Number of degrees of freedom in T-Coupling group rest is 33.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 0 steps, 0.0 ps. 72: 72: NOTE: 38 % of the run time was spent in domain decomposition, 72: 33 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.061 0.015 398.3 72: (ns/day) (hour/ns) 72: Performance: 11.223 2.138 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (29 ms) 72: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (10) 72: 72: Setting the LD random seed to -1663043621 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 72: Number of degrees of freedom in T-Coupling group rest is 1293.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 72: Calculating fourier grid dimensions for X Y Z 72: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 72: 72: Estimate for the relative computational load of the PME mesh part: 0.23 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 2 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 20 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.2%. 72: The balanceable part of the MD step is 23%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.0%. 72: 72: 72: Core t (s) Wall t (s) (%) 72: Time: 1.283 0.321 399.9 72: (ns/day) (hour/ns) 72: Performance: 11.308 2.122 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1625 ms) 72: [----------] 2 tests from BoxDeformationTest (1655 ms total) 72: 72: [----------] 1 test from PositionRestraintCommTest 72: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 72: You have set rlist larger than the interaction cut-off, but you also have 72: verlet-buffer-tolerance > 0. Will set rlist using 72: verlet-buffer-tolerance. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (10) 72: 72: Setting the LD random seed to -730415108 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein' 72: 72: Excluding 3 bonded neighbours molecule type 'OCT' 72: 72: Excluding 1 bonded neighbours molecule type 'NA' 72: 72: Excluding 1 bonded neighbours molecule type 'CL' 72: 72: Excluding 3 bonded neighbours molecule type 'Protein' 72: 72: Excluding 3 bonded neighbours molecule type 'OCT' 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/OctaneSandwich.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 72: 13489 atoms are not part of any of the VCM groups 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 72: 13489 atoms are not part of any center of mass motion removal group. 72: This may lead to artifacts. 72: In most cases one should use one group for the whole system. 72: 72: Number of degrees of freedom in T-Coupling group System is 29527.73 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 72: Removing center of mass motion in the presence of position restraints 72: might cause artifacts. When you are using position restraints to 72: equilibrate a macro-molecule, the artifacts are usually negligible. 72: 72: 72: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: Chain0: 2.207 2.168 7.330 72: Chain1: 2.228 2.186 2.401 72: Chain0: 2.207 2.168 7.330 72: Chain1: 2.228 2.186 2.401 72: 72: This run will generate roughly 1 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Channel_coco in octane membrane' 72: 10 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 6 % of the run time was spent communicating energies, 72: you might want to increase some nst* mdp options 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.684 0.171 399.8 72: (ns/day) (hour/ns) 72: Performance: 11.114 2.159 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (400 ms) 72: [----------] 1 test from PositionRestraintCommTest (400 ms total) 72: 72: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Setting the LD random seed to 2143870393 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file ala.top, line 256]: 72: For energy conservation with LINCS, lincs_iter should be 2 or larger. 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 54.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: The optimal PME mesh load for parallel simulations is below 0.5 72: and for highly parallel simulations between 0.25 and 0.33, 72: for higher performance, increase the cut-off and the PME grid spacing. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: Generated 2211 of the 2211 non-bonded parameter combinations 72: 72: Generated 2211 of the 2211 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 72: 72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 72: Calculating fourier grid dimensions for X Y Z 72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 72: 72: Estimate for the relative computational load of the PME mesh part: 0.95 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'UNNAMED in water' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 13 % of the run time was spent in domain decomposition, 72: 8 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.252 0.063 399.5 72: (ns/day) (hour/ns) 72: Performance: 6.861 3.498 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Setting the LD random seed to -138526983 72: 72: Generated 2211 of the 2211 non-bonded parameter combinations 72: 72: Generated 2211 of the 2211 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: turning H bonds into constraints... 72: 72: NOTE 2 [file ala.top, line 256]: 72: For energy conservation with LINCS, lincs_iter should be 2 or larger. 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 54.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: The optimal PME mesh load for parallel simulations is below 0.5 72: and for highly parallel simulations between 0.25 and 0.33, 72: for higher performance, increase the cut-off and the PME grid spacing. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 72: 72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 72: Calculating fourier grid dimensions for X Y Z 72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 72: 72: Estimate for the relative computational load of the PME mesh part: 0.95 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'UNNAMED in water' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 15 % of the run time was spent in domain decomposition, 72: 9 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.226 0.057 399.5 72: (ns/day) (hour/ns) 72: Performance: 7.621 3.149 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 72: 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 72: 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Generating 1-4 interactions: fudge = 0.5 72: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (24035 ms) 72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 72: Setting the LD random seed to -29378065 72: 72: Generated 2211 of the 2211 non-bonded parameter combinations 72: 72: Generated 2211 of the 2211 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: turning H bonds into constraints... 72: 72: NOTE 2 [file ala.top, line 256]: 72: For energy conservation with LINCS, lincs_iter should be 2 or larger. 72: 72: 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 72: Number of degrees of freedom in T-Coupling group rest is 54.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 72: The optimal PME mesh load for parallel simulations is below 0.5 72: and for highly parallel simulations between 0.25 and 0.33, 72: for higher performance, increase the cut-off and the PME grid spacing. 72: 72: 72: 72: There were 3 NOTEs 72: Calculating fourier grid dimensions for X Y Z 72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 72: 72: Estimate for the relative computational load of the PME mesh part: 0.95 72: 72: This run will generate roughly 0 Mb of data 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'UNNAMED in water' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 12 % of the run time was spent in domain decomposition, 72: 8 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.287 0.072 399.6 72: (ns/day) (hour/ns) 72: Performance: 6.022 3.985 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Setting the LD random seed to -184615169 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file ala.top, line 256]: 72: For energy conservation with LINCS, lincs_iter should be 2 or larger. 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 54.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 72: The optimal PME mesh load for parallel simulations is below 0.5 72: and for highly parallel simulations between 0.25 and 0.33, 72: for higher performance, increase the cut-off and the PME grid spacing. 72: 72: 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 72: Can not increase nstlist because an NVE ensemble is used 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: Generated 2211 of the 2211 non-bonded parameter combinations 72: 72: Generated 2211 of the 2211 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 72: 72: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 72: Calculating fourier grid dimensions for X Y Z 72: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 72: 72: Estimate for the relative computational load of the PME mesh part: 0.95 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'UNNAMED in water' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 16 % of the run time was spent in domain decomposition, 72: 9 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.221 0.055 399.5 72: (ns/day) (hour/ns) 72: Performance: 7.826 3.067 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 72: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (180 ms) 72: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24216 ms total) 72: 72: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 72: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Pull group 1 'FirstWaterMolecule' has 3 atoms 72: Pull group 2 'SecondWaterMolecule' has 3 atoms 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: Pull group natoms pbc atom distance at start reference at t=0 72: 1 3 2 72: 2 3 5 1.112 nm 1.000 nm 72: 72: There was 1 NOTE 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: Setting the LD random seed to -1134301920 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 72: 72: This run will generate roughly 0 Mb of data 72: starting mdrun 'spc2' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 20 % of the run time was spent in domain decomposition, 72: 15 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.135 0.034 399.2 72: (ns/day) (hour/ns) 72: Performance: 12.813 1.873 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Pull group 1 'FirstWaterMolecule' has 3 atoms 72: Pull group 2 'SecondWaterMolecule' has 3 atoms 72: Number of degrees of freedom in T-Coupling group rest is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: Setting the LD random seed to -75563106 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2.gro' 72: Pull group natoms pbc atom distance at start reference at t=0 72: 1 3 2 72: 2 3 5 1.112 nm 1.000 nm 72: 72: There was 1 NOTE 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 72: Can not increase nstlist because an NVE ensemble is used 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: This run will generate roughly 0 Mb of data 72: starting mdrun 'spc2' 72: 4 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 19 % of the run time was spent in domain decomposition, 72: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.149 0.037 399.2 72: (ns/day) (hour/ns) 72: Performance: 11.568 2.075 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 72: [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (103 ms) 72: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (103 ms total) 72: 72: [----------] 12 tests from FreezeWorks/FreezeGroupTest 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 246.451 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 5 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 1.4%. 72: The balanceable part of the MD step is 59%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.8%. 72: 72: 72: NOTE: 22 % of the run time was spent in domain decomposition, 72: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.293 0.074 398.5 72: (ns/day) (hour/ns) 72: Performance: 10.565 2.272 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (96 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 246.451 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 5 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 1.4%. 72: The balanceable part of the MD step is 59%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.8%. 72: 72: 72: NOTE: 22 % of the run time was spent in domain decomposition, 72: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.298 0.075 398.5 72: (ns/day) (hour/ns) 72: Performance: 10.398 2.308 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (97 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: NVE simulation: will use the initial temperature of 246.451 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 5 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 1.3%. 72: The balanceable part of the MD step is 59%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.8%. 72: 72: 72: NOTE: 22 % of the run time was spent in domain decomposition, 72: 13 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.294 0.074 398.5 72: (ns/day) (hour/ns) 72: Performance: 10.554 2.274 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (96 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: NVE simulation: will use the initial temperature of 246.451 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 5 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.5%. 72: The balanceable part of the MD step is 63%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.3%. 72: 72: 72: NOTE: 19 % of the run time was spent in domain decomposition, 72: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.353 0.088 399.6 72: (ns/day) (hour/ns) 72: Performance: 8.807 2.725 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (110 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 246.451 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 5 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.4%. 72: The balanceable part of the MD step is 63%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.2%. 72: 72: 72: NOTE: 19 % of the run time was spent in domain decomposition, 72: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: NOTE: 5 % of the run time was spent communicating energies, 72: you might want to increase some nst* mdp options 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.355 0.089 399.6 72: (ns/day) (hour/ns) 72: Performance: 8.751 2.743 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (111 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 72: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in domain decomposition, 72: 6 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.292 0.073 397.5 72: (ns/day) (hour/ns) 72: Performance: 10.589 2.266 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (98 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in domain decomposition, 72: 6 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.298 0.075 399.5 72: (ns/day) (hour/ns) 72: Performance: 10.426 2.302 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (99 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vacuo.gro' 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in domain decomposition, 72: 6 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.294 0.074 398.5 72: (ns/day) (hour/ns) 72: Performance: 10.527 2.280 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (100 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 13 % of the run time was spent in domain decomposition, 72: 8 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.246 0.061 399.5 72: (ns/day) (hour/ns) 72: Performance: 12.647 1.898 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (99 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 22 % of the run time was spent in domain decomposition, 72: 12 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.154 0.042 363.7 72: (ns/day) (hour/ns) 72: Performance: 18.365 1.307 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (81 ms) 72: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 72: 72: turning H bonds into constraints... 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 72: There are 5 atoms that are fully frozen and part of COMM removal 72: group(s), removing these atoms from the COMM removal group(s) 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 72: There are 3 atoms that are frozen along less then 3 dimensions and part 72: of COMM removal group(s), due to limitations in the code these still 72: contribute to the mass of the COM along frozen dimensions and therefore 72: the COMM correction will be too small. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 72: 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine-dipeptide' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: NOTE: 11 % of the run time was spent in domain decomposition, 72: 10 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.277 0.069 398.4 72: (ns/day) (hour/ns) 72: Performance: 11.195 2.144 72: 72: 72: 72: 72: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (207 ms) 72: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1201 ms total) 72: 72: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generated 3 of the 3 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Setting gen_seed to 2147205079 72: 72: Velocities were taken from a Maxwell distribution at 0 K 72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: Net Acceleration in X direction, will not be corrected 72: Net Acceleration in Y direction, will not be corrected 72: Net Acceleration in Z direction, will not be corrected 72: 72: This run will generate roughly 0 Mb of data 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.0%. 72: The balanceable part of the MD step is 58%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.0%. 72: 72: 72: NOTE: 24 % of the run time was spent in domain decomposition, 72: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.234 0.058 399.5 72: (ns/day) (hour/ns) 72: Performance: 26.591 0.903 72: 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 72: Net Acceleration in X direction, will not be corrected 72: Net Acceleration in Y direction, will not be corrected 72: Net Acceleration in Z direction, will not be corrected 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because verlet-buffer-tolerance is not set or used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (73 ms) 72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Setting gen_seed to -803345 72: 72: Velocities were taken from a Maxwell distribution at 0 K 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.0%. 72: The balanceable part of the MD step is 58%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.0%. 72: 72: 72: NOTE: 25 % of the run time was spent in domain decomposition, 72: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.234 0.059 399.5 72: (ns/day) (hour/ns) 72: Performance: 26.520 0.905 72: 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: Net Acceleration in X direction, will not be corrected 72: Net Acceleration in Y direction, will not be corrected 72: Net Acceleration in Z direction, will not be corrected 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: 72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (72 ms) 72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Setting gen_seed to -291902215 72: 72: Velocities were taken from a Maxwell distribution at 0 K 72: 72: This run will generate roughly 0 Mb of data 72: Can not increase nstlist because an NVE ensemble is used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 0.0%. 72: The balanceable part of the MD step is 62%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 0.0%. 72: 72: 72: NOTE: 21 % of the run time was spent in domain decomposition, 72: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.275 0.069 399.6 72: (ns/day) (hour/ns) 72: Performance: 22.589 1.062 72: 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 72: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 72: < 0 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 72: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 72: Net Acceleration in X direction, will not be corrected 72: Net Acceleration in Y direction, will not be corrected 72: Net Acceleration in Z direction, will not be corrected 72: 72: There were 3 NOTEs 72: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 72: Can not increase nstlist because verlet-buffer-tolerance is not set or used 72: Using 2 MPI processes 72: Using 2 OpenMP threads per MPI process 72: 72: 72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (82 ms) 72: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Setting gen_seed to -273688588 72: 72: Velocities were taken from a Maxwell distribution at 0 K 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 8 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: 72: Dynamic load balancing report: 72: DLB was off during the run due to low measured imbalance. 72: Average load imbalance: 48.7%. 72: The balanceable part of the MD step is 42%, load imbalance is computed from this. 72: Part of the total run time spent waiting due to load imbalance: 20.3%. 72: 72: NOTE: 20.3 % of the available CPU time was lost due to load imbalance 72: in the domain decomposition. 72: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 72: You can also consider manually changing the decomposition (option -dd); 72: e.g. by using fewer domains along the box dimension in which there is 72: considerable inhomogeneity in the simulated system. 72: 72: NOTE: 16 % of the run time was spent in domain decomposition, 72: 3 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: NOTE: 9 % of the run time was spent communicating energies, 72: you might want to increase some nst* mdp options 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.915 0.229 399.9 72: (ns/day) (hour/ns) 72: Performance: 6.794 3.533 72: 72: 72: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (243 ms) 72: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (472 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 29 tests from 8 test suites ran. (29126 ms total) 72: [ PASSED ] 28 tests. 72: [ SKIPPED ] 1 test, listed below: 72: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 72/96 Test #72: MdrunTestsTwoRanks ........................... Passed 29.47 sec test 73 Start 73: MdrunSingleRankAlgorithmsTests 73: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 5 tests from 3 test suites. 73: [----------] Global test environment set-up. 73: [----------] 1 test from DispersionCorrectionTest 73: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 30.00 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 73: There are 9 non-linear virtual site constructions. Their contribution to 73: the energy error is approximated. In most cases this does not affect the 73: error significantly. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 2 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 73: 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 1 MPI process 73: Using 2 OpenMP threads 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Alanine dipeptide in vacuo' 73: 200 steps, 0.4 ps. 73: Setting the LD random seed to -2000385 73: 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning H bonds into constraints... 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Converted 3 Bonds with virtual sites to connections, 7 left 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 12 Constraints with virtual sites to connections, 0 left 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.034 0.017 199.2 73: (ns/day) (hour/ns) 73: Performance: 2064.215 0.012 73: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (48 ms) 73: [----------] 1 test from DispersionCorrectionTest (48 ms total) 73: 73: [----------] 1 test from OriresTest 73: [ RUN ] OriresTest.OriresCanRun 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 518.00 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There was 1 NOTE 73: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 73: 73: Using 1 MPI process 73: Using 2 OpenMP threads 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 73: 10 steps, 0.0 ps. 73: Setting the LD random seed to 1794047677 73: 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 73: 73: turning H bonds into constraints... 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: turning H bonds into constraints... 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/orires_1lvz.gro' 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 195.4 73: (ns/day) (hour/ns) 73: Performance: 984.750 0.024 73: [ OK ] OriresTest.OriresCanRun (261 ms) 73: [----------] 1 test from OriresTest (261 ms total) 73: 73: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 73: Number of degrees of freedom in T-Coupling group rest is 10.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: There were 2 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 1 MPI process 73: Using 2 OpenMP threads 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Dipoles' 73: 20 steps, 0.1 ps. 73: Setting the LD random seed to -1158758411 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Dipole' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 73: 73: Searching the wall atom type(s) 73: 73: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.423 0.212 199.9 73: (ns/day) (hour/ns) 73: Performance: 21.429 1.120 73: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 73: 73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (40510 ms) 73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 73: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 73: The supported numbers are > 1. 73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 73: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 73: With epsilon_surface > 0 all molecules should be neutral. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 73: With epsilon_surface > 0 you can only use domain decomposition when there 73: are only small molecules with all bonds constrained (mdrun will check for 73: this). 73: 73: Number of degrees of freedom in T-Coupling group rest is 9.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: There were 4 NOTEs 73: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 1 MPI process 73: Using 2 OpenMP threads 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Dipoles' 73: 20 steps, 0.1 ps. 73: Setting the LD random seed to -620889089 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Dipole' 73: 73: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 73: 73: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.017 0.009 198.6 73: (ns/day) (hour/ns) 73: Performance: 515.397 0.047 73: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 73: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (19512 ms) 73: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (60023 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 5 tests from 3 test suites ran. (60345 ms total) 73: [ PASSED ] 5 tests. 73/96 Test #73: MdrunSingleRankAlgorithmsTests ............... Passed 60.64 sec test 74 Start 74: Minimize1RankTests 74: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/Minimize1RankTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 12 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Steepest Descents: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Steepest Descents did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = -4.7990997e+01 74: Maximum force = 1.8629692e+02 on atom 13 74: Norm of force = 8.7721836e+01 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (207 ms) 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Polak-Ribiere Conjugate Gradients: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: F-max = 3.02331e+02 on atom 3 74: F-Norm = 1.18024e+02 74: 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = -5.5862350e+01 74: Maximum force = 4.2726685e+02 on atom 13 74: Norm of force = 1.8452681e+02 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (222 ms) 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 1 74: Number of degrees of freedom in T-Coupling group System is 22.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Glycine' 74: 74: turning H bonds into constraints... 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Steepest Descents: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Steepest Descents did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = 3.1937723e+02 74: Maximum force = 9.9988691e+03 on atom 9 74: Norm of force = 4.6167015e+03 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (85 ms) 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 1 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Glycine' 74: 74: turning H bonds into constraints... 74: 74: NOTE 3 [file glycine_vacuo.top, line 12]: 74: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 74: 74: Number of degrees of freedom in T-Coupling group System is 22.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Polak-Ribiere Conjugate Gradients: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: F-max = 2.41575e+04 on atom 10 74: F-Norm = 1.18451e+04 74: 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = 1.5174414e+02 74: Maximum force = 7.4208760e+03 on atom 9 74: Norm of force = 3.5692977e+03 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (94 ms) 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 5 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Steepest Descents: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Steepest Descents did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = -1.5698444e+02 74: Maximum force = 4.5702216e+02 on atom 17 74: Norm of force = 1.8327095e+02 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: 74: NOTE 4 [file unknown]: 74: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 6 NOTEs 74: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (80 ms) 74: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Polak-Ribiere Conjugate Gradients: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: F-max = 1.06799e+03 on atom 28 74: F-Norm = 4.26914e+02 74: 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = -1.6941290e+02 74: Maximum force = 2.1840109e+02 on atom 17 74: Norm of force = 7.9232004e+01 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (112 ms) 74: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (805 ms total) 74: 74: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Steepest Descents: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: writing lowest energy coordinates. 74: 74: Steepest Descents converged to Fmax < 10 in 1 steps 74: Potential Energy = -9.7425687e-01 74: Maximum force = 4.0132279e+00 on atom 1 74: Norm of force = 1.6383933e+00 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (12 ms) 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Polak-Ribiere Conjugate Gradients: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: F-max = 4.01323e+00 on atom 1 74: F-Norm = 1.63839e+00 74: 74: 74: writing lowest energy coordinates. 74: 74: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 74: Potential Energy = -9.9064195e-01 74: Maximum force = 2.5781672e+00 on atom 1 74: Norm of force = 1.0525324e+00 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (15 ms) 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 3 NOTEs 74: 74: There was 1 WARNING 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Low-Memory BFGS Minimizer: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: Using 10 BFGS correction steps. 74: 74: F-max = 4.01323e+00 on atom 1 74: F-Norm = 1.63839e+00 74: 74: 74: writing lowest energy coordinates. 74: 74: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 74: Potential Energy = -9.9064195e-01 74: Maximum force = 2.5781672e+00 on atom 1 74: Norm of force = 1.0525324e+00 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms) 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 1 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Glycine' 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: This run will generate roughly 0 Mb of data 74: 74: Steepest Descents: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Steepest Descents did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = 3.1939673e+02 74: Maximum force = 9.9704229e+03 on atom 9 74: Norm of force = 4.6227534e+03 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (79 ms) 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 1 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Glycine' 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Polak-Ribiere Conjugate Gradients: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: 74: This run will generate roughly 0 Mb of data 74: F-max = 2.41672e+04 on atom 10 74: F-Norm = 1.19357e+04 74: 74: 74: Energy minimization reached the maximum number of steps before the forces 74: reached the requested precision Fmax < 10. 74: 74: writing lowest energy coordinates. 74: 74: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 74: Potential Energy = 1.5625757e+02 74: Maximum force = 7.5018242e+03 on atom 9 74: Norm of force = 3.6139019e+03 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (84 ms) 74: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 74: 74: Generated 20503 of the 20503 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 1 74: 74: Generated 17396 of the 20503 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Glycine' 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 74: COM removal frequency is set to (4). 74: Other settings require a global communication frequency of 100. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 100. 74: 74: 74: There were 4 NOTEs 74: 74: There was 1 WARNING 74: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: Low-Memory BFGS Minimizer: 74: Tolerance (Fmax) = 1.00000e+01 74: Number of steps = 4 74: Using 10 BFGS correction steps. 74: 74: F-max = 2.41672e+04 on atom 10 74: F-Norm = 1.19357e+04 74: 74: 74: Energy minimization has stopped, but the forces have not converged to the 74: requested precision Fmax < 10 (which may not be possible for your system). It 74: stopped because the algorithm tried to make a new step whose size was too 74: small, or there was no change in the energy since last step. Either way, we 74: regard the minimization as converged to within the available machine 74: precision, given your starting configuration and EM parameters. 74: 74: Double precision normally gives you higher accuracy, but this is often not 74: needed for preparing to run molecular dynamics. 74: 74: writing lowest energy coordinates. 74: 74: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 74: but did not reach the requested Fmax < 10. 74: Potential Energy = 5.6111609e+02 74: Maximum force = 1.2685385e+04 on atom 10 74: Norm of force = 6.0643598e+03 74: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (80 ms) 74: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (289 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 12 tests from 2 test suites ran. (1105 ms total) 74: [ PASSED ] 12 tests. 74/96 Test #74: Minimize1RankTests ........................... Passed 1.38 sec test 75 Start 75: Minimize2RankTests 75: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/Minimize2RankTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 12 tests from 2 test suites. 75: [----------] Global test environment set-up. 75: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 330891 of the 330891 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 330891 of the 330891 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: Number of degrees of freedom in T-Coupling group System is 27.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Steepest Descents: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Steepest Descents did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = -4.7990952e+01 75: Maximum force = 1.8629709e+02 on atom 13 75: Norm of force = 8.7721970e+01 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (331 ms) 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 330891 of the 330891 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 330891 of the 330891 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: Number of degrees of freedom in T-Coupling group System is 27.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: 75: This run will generate roughly 0 Mb of data 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Polak-Ribiere Conjugate Gradients: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: F-max = 3.02331e+02 on atom 3 75: F-Norm = 1.18024e+02 75: 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = -5.5862202e+01 75: Maximum force = 4.2727243e+02 on atom 13 75: Norm of force = 1.8452909e+02 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (292 ms) 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 75: Generated 20503 of the 20503 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 1 75: 75: Generated 17396 of the 20503 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Glycine' 75: 75: turning H bonds into constraints... 75: Number of degrees of freedom in T-Coupling group System is 22.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Steepest Descents: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Steepest Descents did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = 3.1937720e+02 75: Maximum force = 9.9988691e+03 on atom 9 75: Norm of force = 4.6167015e+03 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (121 ms) 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 75: Generated 20503 of the 20503 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 1 75: 75: Generated 17396 of the 20503 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Glycine' 75: 75: turning H bonds into constraints... 75: 75: NOTE 3 [file glycine_vacuo.top, line 12]: 75: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 75: 75: Number of degrees of freedom in T-Coupling group System is 22.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 5 NOTEs 75: 75: This run will generate roughly 0 Mb of data 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Polak-Ribiere Conjugate Gradients: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: F-max = 2.41575e+04 on atom 10 75: F-Norm = 1.18451e+04 75: 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = 1.5174358e+02 75: Maximum force = 7.4208833e+03 on atom 9 75: Norm of force = 3.5692986e+03 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generating 1-4 interactions: fudge = 0.5 75: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (128 ms) 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 75: Generated 2145 of the 2145 non-bonded parameter combinations 75: 75: Generated 2145 of the 2145 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 75: 75: turning all bonds into constraints... 75: 75: Cleaning up constraints and constant bonded interactions with virtual sites 75: 75: Removed 18 Angles with virtual sites, 21 left 75: 75: Removed 10 Proper Dih.s with virtual sites, 44 left 75: 75: Converted 15 Constraints with virtual sites to connections, 7 left 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file unknown]: 75: You are using constraints on all bonds, whereas the forcefield has been 75: parametrized only with constraints involving hydrogen atoms. We suggest 75: using constraints = h-bonds instead, this will also improve performance. 75: 75: Number of degrees of freedom in T-Coupling group System is 23.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 5 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Update groups can not be used for this system because an incompatible virtual site type is used 75: 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Steepest Descents: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Steepest Descents did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = -1.5698444e+02 75: Maximum force = 4.5702222e+02 on atom 17 75: Norm of force = 1.8327095e+02 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generating 1-4 interactions: fudge = 0.5 75: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (107 ms) 75: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 75: Generated 2145 of the 2145 non-bonded parameter combinations 75: 75: Generated 2145 of the 2145 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 75: 75: turning all bonds into constraints... 75: 75: NOTE 3 [file unknown]: 75: You are using constraints on all bonds, whereas the forcefield has been 75: parametrized only with constraints involving hydrogen atoms. We suggest 75: using constraints = h-bonds instead, this will also improve performance. 75: 75: 75: NOTE 4 [file unknown]: 75: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 75: 75: Number of degrees of freedom in T-Coupling group System is 23.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 6 NOTEs 75: 75: Cleaning up constraints and constant bonded interactions with virtual sites 75: 75: Removed 18 Angles with virtual sites, 21 left 75: 75: Removed 10 Proper Dih.s with virtual sites, 44 left 75: 75: Converted 15 Constraints with virtual sites to connections, 7 left 75: 75: This run will generate roughly 0 Mb of data 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Update groups can not be used for this system because an incompatible virtual site type is used 75: 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Polak-Ribiere Conjugate Gradients: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: F-max = 1.06799e+03 on atom 28 75: F-Norm = 4.26914e+02 75: 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = -1.6941266e+02 75: Maximum force = 2.1838609e+02 on atom 17 75: Norm of force = 7.9233324e+01 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (333 ms) 75: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1320 ms total) 75: 75: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 3 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Steepest Descents: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: 75: writing lowest energy coordinates. 75: 75: Steepest Descents converged to Fmax < 10 in 1 steps 75: Potential Energy = -9.7425687e-01 75: Maximum force = 4.0132279e+00 on atom 3 75: Norm of force = 1.6383933e+00 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (25 ms) 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 3 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Polak-Ribiere Conjugate Gradients: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: F-max = 4.01323e+00 on atom 3 75: F-Norm = 1.63839e+00 75: 75: 75: writing lowest energy coordinates. 75: 75: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 75: Potential Energy = -9.9064195e-01 75: Maximum force = 2.5781672e+00 on atom 3 75: Norm of force = 1.0525324e+00 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 3 NOTEs 75: 75: There was 1 WARNING 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (45 ms) 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 75: Generated 20503 of the 20503 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 1 75: 75: Generated 17396 of the 20503 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Glycine' 75: Number of degrees of freedom in T-Coupling group System is 27.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Steepest Descents: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Steepest Descents did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = 3.1939664e+02 75: Maximum force = 9.9704229e+03 on atom 9 75: Norm of force = 4.6227537e+03 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (112 ms) 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 75: Generated 20503 of the 20503 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 1 75: 75: Generated 17396 of the 20503 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Glycine' 75: Number of degrees of freedom in T-Coupling group System is 27.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 75: Using 2 MPI processes 75: Using 2 OpenMP threads per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: Polak-Ribiere Conjugate Gradients: 75: Tolerance (Fmax) = 1.00000e+01 75: Number of steps = 4 75: F-max = 2.41672e+04 on atom 10 75: F-Norm = 1.19357e+04 75: 75: 75: Energy minimization reached the maximum number of steps before the forces 75: reached the requested precision Fmax < 10. 75: 75: writing lowest energy coordinates. 75: 75: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 75: Potential Energy = 1.5625771e+02 75: Maximum force = 7.5018237e+03 on atom 9 75: Norm of force = 3.6139019e+03 75: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (120 ms) 75: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 75: 75: Generated 20503 of the 20503 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 1 75: 75: Generated 17396 of the 20503 1-4 parameter combinations 75: 75: Excluding 3 bonded neighbours molecule type 'Glycine' 75: Number of degrees of freedom in T-Coupling group System is 27.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 75: COM removal frequency is set to (4). 75: Other settings require a global communication frequency of 100. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 100. 75: 75: 75: There were 4 NOTEs 75: 75: There was 1 WARNING 75: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (48 ms) 75: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (356 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 12 tests from 2 test suites ran. (1689 ms total) 75: [ PASSED ] 12 tests. 75/96 Test #75: Minimize2RankTests ........................... Passed 2.11 sec test 76 Start 76: MdrunNonIntegratorTests 76: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 46 tests from 3 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from NonbondedBenchTest 76: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 76: SIMD width: 4 76: System size: 3000 atoms 76: Cut-off radius: 1 nm 76: Number of threads: 1 76: Number of iterations: 1 76: Compute energies: no 76: Ewald excl. corr.: analytical 76: 76: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 76: total useful 76: Ewald all geom. 4xM 0.116 0.1165 10.2206 5.4072 76: [ OK ] NonbondedBenchTest.BasicEndToEndTest (15 ms) 76: [----------] 1 test from NonbondedBenchTest (15 ms total) 76: 76: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.008 0.004 196.8 76: (ns/day) (hour/ns) 76: Performance: 364.683 0.066 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 76: 76: trr version: GMX_trn_file (single precision) 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 48 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.031 199.8 76: (ns/day) (hour/ns) 76: Performance: 46.719 0.514 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (96 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 21 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.153 0.077 199.9 76: (ns/day) (hour/ns) 76: Performance: 19.189 1.251 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 62 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.046 0.023 199.8 76: (ns/day) (hour/ns) 76: Performance: 63.776 0.376 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (107 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.113 0.057 199.8 76: (ns/day) (hour/ns) 76: Performance: 25.921 0.926 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 58 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.050 0.025 199.8 76: (ns/day) (hour/ns) 76: Performance: 58.583 0.410 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (92 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.114 0.057 199.8 76: (ns/day) (hour/ns) 76: Performance: 25.781 0.931 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 57 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.050 0.025 199.8 76: (ns/day) (hour/ns) 76: Performance: 58.277 0.412 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (92 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.133 0.067 199.8 76: (ns/day) (hour/ns) 76: Performance: 22.018 1.090 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 59 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.042 0.021 199.7 76: (ns/day) (hour/ns) 76: Performance: 69.701 0.344 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (254 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.166 0.083 199.9 76: (ns/day) (hour/ns) 76: Performance: 17.736 1.353 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 59 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.042 0.021 199.7 76: (ns/day) (hour/ns) 76: Performance: 69.847 0.344 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (257 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.130 0.065 199.8 76: (ns/day) (hour/ns) 76: Performance: 22.538 1.065 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 57 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.050 0.025 199.8 76: (ns/day) (hour/ns) 76: Performance: 59.081 0.406 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (247 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.154 0.077 199.9 76: (ns/day) (hour/ns) 76: Performance: 19.018 1.262 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 54 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.046 0.023 199.8 76: (ns/day) (hour/ns) 76: Performance: 63.762 0.376 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (258 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: 76: NOTE 3 [file unknown]: 76: You are using constraints on all bonds, whereas the forcefield has been 76: parametrized only with constraints involving hydrogen atoms. We suggest 76: using constraints = h-bonds instead, this will also improve performance. 76: 76: Number of degrees of freedom in T-Coupling group System is 23.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 76: NVE simulation: will use the initial temperature of 456.887 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 76: There are 9 non-linear virtual site constructions. Their contribution to 76: the energy error is approximated. In most cases this does not affect the 76: error significantly. 76: 76: 76: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 6 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Alanine dipeptide in vacuo' 76: 16 steps, 0.0 ps. 76: Generated 2145 of the 2145 non-bonded parameter combinations 76: 76: Generated 2145 of the 2145 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 76: 76: turning all bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 76: 76: Cleaning up constraints and constant bonded interactions with virtual sites 76: 76: Removed 18 Angles with virtual sites, 21 left 76: 76: Removed 10 Proper Dih.s with virtual sites, 44 left 76: 76: Converted 15 Constraints with virtual sites to connections, 7 left 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.202 0.101 199.9 76: (ns/day) (hour/ns) 76: Performance: 14.563 1.648 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 19 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.001 190.4 76: (ns/day) (hour/ns) 76: Performance: 2558.386 0.009 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (158 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: 76: NOTE 3 [file unknown]: 76: You are using constraints on all bonds, whereas the forcefield has been 76: parametrized only with constraints involving hydrogen atoms. We suggest 76: using constraints = h-bonds instead, this will also improve performance. 76: 76: Number of degrees of freedom in T-Coupling group System is 23.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 76: NVE simulation: will use the initial temperature of 456.887 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 76: There are 9 non-linear virtual site constructions. Their contribution to 76: the energy error is approximated. In most cases this does not affect the 76: error significantly. 76: 76: 76: NOTE 6 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 6 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Alanine dipeptide in vacuo' 76: 16 steps, 0.0 ps. 76: Generated 2145 of the 2145 non-bonded parameter combinations 76: 76: Generated 2145 of the 2145 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 76: 76: turning all bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 76: 76: Cleaning up constraints and constant bonded interactions with virtual sites 76: 76: Removed 18 Angles with virtual sites, 21 left 76: 76: Removed 10 Proper Dih.s with virtual sites, 44 left 76: 76: Converted 15 Constraints with virtual sites to connections, 7 left 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.032 0.016 199.1 76: (ns/day) (hour/ns) 76: Performance: 92.005 0.261 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 44 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.074 0.037 199.8 76: (ns/day) (hour/ns) 76: Performance: 39.614 0.606 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (119 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: 76: NOTE 3 [file unknown]: 76: You are using constraints on all bonds, whereas the forcefield has been 76: parametrized only with constraints involving hydrogen atoms. We suggest 76: using constraints = h-bonds instead, this will also improve performance. 76: 76: Number of degrees of freedom in T-Coupling group System is 23.00 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 76: There are 9 non-linear virtual site constructions. Their contribution to 76: the energy error is approximated. In most cases this does not affect the 76: error significantly. 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 5 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 76: 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Alanine dipeptide in vacuo' 76: 16 steps, 0.0 ps. 76: Generated 2145 of the 2145 non-bonded parameter combinations 76: 76: Generated 2145 of the 2145 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 76: 76: turning all bonds into constraints... 76: 76: Cleaning up constraints and constant bonded interactions with virtual sites 76: 76: Removed 18 Angles with virtual sites, 21 left 76: 76: Removed 10 Proper Dih.s with virtual sites, 44 left 76: 76: Converted 15 Constraints with virtual sites to connections, 7 left 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.439 0.220 200.0 76: (ns/day) (hour/ns) 76: Performance: 6.684 3.590 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 76: 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 47 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.069 0.035 199.8 76: (ns/day) (hour/ns) 76: Performance: 42.333 0.567 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (337 ms) 76: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: 76: NOTE 3 [file unknown]: 76: You are using constraints on all bonds, whereas the forcefield has been 76: parametrized only with constraints involving hydrogen atoms. We suggest 76: using constraints = h-bonds instead, this will also improve performance. 76: 76: Number of degrees of freedom in T-Coupling group System is 23.00 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 76: There are 9 non-linear virtual site constructions. Their contribution to 76: the energy error is approximated. In most cases this does not affect the 76: error significantly. 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 5 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 76: 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Alanine dipeptide in vacuo' 76: 16 steps, 0.0 ps. 76: Generated 2145 of the 2145 non-bonded parameter combinations 76: 76: Generated 2145 of the 2145 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 76: 76: turning all bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 76: 76: Cleaning up constraints and constant bonded interactions with virtual sites 76: 76: Removed 18 Angles with virtual sites, 21 left 76: 76: Removed 10 Proper Dih.s with virtual sites, 44 left 76: 76: Converted 15 Constraints with virtual sites to connections, 7 left 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.646 0.323 200.0 76: (ns/day) (hour/ns) 76: Performance: 4.547 5.278 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 76: 76: Update groups can not be used for this system because an incompatible virtual site type is used 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 48 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.070 0.035 199.8 76: (ns/day) (hour/ns) 76: Performance: 42.199 0.569 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (411 ms) 76: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2434 ms total) 76: 76: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.182 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.133 1.488 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.677 0.483 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (142 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.181 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.213 1.480 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.550 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (141 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.181 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.201 1.481 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.403 0.486 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (141 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.176 0.088 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.647 1.442 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 19 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.001 189.1 76: (ns/day) (hour/ns) 76: Performance: 2039.932 0.012 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (149 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.052 0.026 199.4 76: (ns/day) (hour/ns) 76: Performance: 55.917 0.429 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 37 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.088 0.044 199.8 76: (ns/day) (hour/ns) 76: Performance: 33.164 0.724 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (134 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.182 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.112 1.490 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.476 0.485 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (142 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.182 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.147 1.486 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.648 0.483 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (141 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.181 0.090 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.235 1.478 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 59 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.056 0.028 199.7 76: (ns/day) (hour/ns) 76: Performance: 52.483 0.457 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (140 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.240 0.120 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.237 1.961 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 54 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.062 0.031 199.7 76: (ns/day) (hour/ns) 76: Performance: 47.652 0.504 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (220 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.182 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.137 1.487 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.454 0.485 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (142 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.181 0.091 199.8 76: (ns/day) (hour/ns) 76: Performance: 16.200 1.481 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.567 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (141 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.770 1.879 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 55 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.060 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.070 0.489 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (163 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.229 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.813 1.873 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.532 0.485 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (162 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.775 1.879 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 50 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.014 0.007 198.9 76: (ns/day) (hour/ns) 76: Performance: 201.610 0.119 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (141 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.746 1.883 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.060 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 48.488 0.495 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (164 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.782 1.878 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.616 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (163 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.756 1.881 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.459 0.485 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (163 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.229 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.803 1.874 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 55 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.029 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.950 0.480 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (162 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.229 0.114 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.837 1.870 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.573 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (162 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.793 1.876 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.6 76: (ns/day) (hour/ns) 76: Performance: 49.514 0.485 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (163 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.230 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.787 1.877 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.615 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (163 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 76: NVE simulation: will use the initial temperature of 294.908 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.229 0.115 199.9 76: (ns/day) (hour/ns) 76: Performance: 12.822 1.872 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 56 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.059 0.030 199.7 76: (ns/day) (hour/ns) 76: Performance: 49.635 0.484 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (162 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.106 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.801 1.739 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.031 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.647 0.514 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (165 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.107 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.775 1.742 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.267 0.519 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (166 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.212 0.106 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.816 1.737 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 47 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.097 0.049 199.8 76: (ns/day) (hour/ns) 76: Performance: 30.270 0.793 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (189 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.225 0.112 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.073 1.836 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.309 0.518 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (197 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.214 0.107 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.728 1.748 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.343 0.518 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (166 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.211 0.106 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.895 1.727 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.031 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.729 0.514 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (165 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.013 0.007 198.0 76: (ns/day) (hour/ns) 76: Performance: 223.307 0.107 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.064 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.153 0.520 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (69 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.106 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.800 1.739 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.266 0.519 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (166 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.107 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.771 1.743 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 53 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.064 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 45.864 0.523 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (166 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.107 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.775 1.742 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 52 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 46.420 0.517 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (166 ms) 76: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 79.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun '30 atom system in water' 76: 16 steps, 0.0 ps. 76: Generated 2485 of the 2485 non-bonded parameter combinations 76: 76: Generated 2485 of the 2485 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'nonanol' 76: 76: turning H bonds into constraints... 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: turning H bonds into constraints... 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.213 0.107 199.9 76: (ns/day) (hour/ns) 76: Performance: 13.791 1.740 76: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 76: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 76: 76: Using 1 MPI process 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 76: 76: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 76: 76: NOTE: 53 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.064 0.032 199.7 76: (ns/day) (hour/ns) 76: Performance: 45.805 0.524 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 76: 76: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (166 ms) 76: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5199 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 46 tests from 3 test suites ran. (7657 ms total) 76: [ PASSED ] 46 tests. 76/96 Test #76: MdrunNonIntegratorTests ...................... Passed 7.80 sec test 77 Start 77: MdrunTpiTests 77: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 3 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 3 tests from Simple/TpiTest 77: [ RUN ] Simple/TpiTest.ReproducesOutput/0 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 1308.00 77: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 77: TPI is not implemented for GPUs. 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: Reading frames from gro file '216 water molecules', 648 atoms. 77: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 77: Last frame 0 time 0.000 77: Generated 331705 of the 331705 non-bonded parameter combinations 77: 77: Generated 331705 of the 331705 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Excluding 3 bonded neighbours molecule type 'methane' 77: Analysing residue names: 77: There are: 216 Water residues 77: There are: 1 Other residues 77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] Simple/TpiTest.ReproducesOutput/0 (177 ms) 77: [ RUN ] Simple/TpiTest.ReproducesOutput/1 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 1308.00 77: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 77: TPI is not implemented for GPUs. 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: Reading frames from gro file '216 water molecules', 648 atoms. 77: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 77: Last frame 0 time 0.000 77: Generated 331705 of the 331705 non-bonded parameter combinations 77: 77: Generated 331705 of the 331705 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Excluding 3 bonded neighbours molecule type 'methane' 77: Analysing residue names: 77: There are: 216 Water residues 77: There are: 1 Other residues 77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] Simple/TpiTest.ReproducesOutput/1 (166 ms) 77: [ RUN ] Simple/TpiTest.ReproducesOutput/2 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 1308.00 77: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 77: TPI is not implemented for GPUs. 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: Reading frames from gro file '216 water molecules', 648 atoms. 77: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 77: Last frame 0 time 0.000 77: Generated 331705 of the 331705 non-bonded parameter combinations 77: 77: Generated 331705 of the 331705 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Excluding 3 bonded neighbours molecule type 'methane' 77: Analysing residue names: 77: There are: 216 Water residues 77: There are: 1 Other residues 77: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] Simple/TpiTest.ReproducesOutput/2 (169 ms) 77: [----------] 3 tests from Simple/TpiTest (513 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 3 tests from 1 test suite ran. (517 ms total) 77: [ PASSED ] 3 tests. 77/96 Test #77: MdrunTpiTests ................................ Passed 0.70 sec test 78 Start 78: MdrunMpiTests 78: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 16 tests from 2 test suites. 78: [----------] Global test environment set-up. 78: [----------] 4 tests from MimicTest 78: [ RUN ] MimicTest.OneQuantumMol 78: Setting the LD random seed to -1640015493 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: 78: This run will generate roughly 0 Mb of data 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 39 % of the run time was spent in domain decomposition, 78: 38 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.079 0.020 399.5 78: (ns/day) (hour/ns) 78: Performance: 4.376 5.484 78: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (81 ms) 78: [ RUN ] MimicTest.AllQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Setting the LD random seed to -1210253394 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 53 % of the run time was spent in domain decomposition, 78: 32 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.057 0.014 399.3 78: (ns/day) (hour/ns) 78: Performance: 6.088 3.942 78: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (36 ms) 78: [ RUN ] MimicTest.TwoQuantumMol 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Setting the LD random seed to -1640519158 78: 78: Generated 10 of the 10 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 10 of the 10 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group rest is 21.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/4water.gro' 78: 78: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 34 % of the run time was spent in domain decomposition, 78: 40 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.088 0.022 398.4 78: (ns/day) (hour/ns) 78: Performance: 3.905 6.145 78: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (41 ms) 78: [ RUN ] MimicTest.BondCuts 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Setting the LD random seed to 1946147835 78: 78: Generated 2211 of the 2211 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 2211 of the 2211 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 78: Number of degrees of freedom in T-Coupling group rest is 66.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: NVE simulation: will use the initial temperature of 300.368 K for 78: determining the Verlet buffer size 78: 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/ala.gro' 78: 78: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 78: Reading frame 0 time 0.000 Last frame 0 time 0.000 78: 78: NOTE: 31 % of the run time was spent in domain decomposition, 78: 7 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 18 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.148 0.037 399.7 78: (ns/day) (hour/ns) 78: Performance: 2.336 10.273 78: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (83 ms) 78: [----------] 4 tests from MimicTest (254 ms total) 78: 78: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 78: Setting the LD random seed to -1082524713 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group rest is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There was 1 NOTE 78: Setting the LD random seed to -268439568 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -541641 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group rest is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 78: NVE simulation with an initial temperature of zero: will use a Verlet 78: buffer of 10%. Check your energy drift! 78: 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 2 NOTEs 78: Setting the LD random seed to -1084248129 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There was 1 NOTE 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.3%. 78: The balanceable part of the MD step is 62%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.2%. 78: 78: 78: NOTE: 18 % of the run time was spent in domain decomposition, 78: 9 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 6 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.645 0.161 399.8 78: (ns/day) (hour/ns) 78: Performance: 11.241 2.135 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 78: 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (196 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE: 7 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.586 0.147 399.2 78: (ns/day) (hour/ns) 78: Performance: 12.364 1.941 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (160 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 3.2%. 78: The balanceable part of the MD step is 22%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.7%. 78: 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.437 0.359 399.9 78: (ns/day) (hour/ns) 78: Performance: 5.051 4.752 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (11567 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.544 0.136 399.6 78: (ns/day) (hour/ns) 78: Performance: 13.336 1.800 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (6220 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.797 0.199 399.9 78: (ns/day) (hour/ns) 78: Performance: 9.108 2.635 78: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (224 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.009 0.252 399.8 78: (ns/day) (hour/ns) 78: Performance: 7.186 3.340 78: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (278 ms) 78: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 78: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (18648 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 16 tests from 2 test suites ran. (18949 ms total) 78: [ PASSED ] 10 tests. 78: [ SKIPPED ] 6 tests, listed below: 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 78: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 78/96 Test #78: MdrunMpiTests ................................ Passed 19.38 sec test 79 Start 79: MdrunMultiSimTests 79: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 6 tests from 2 test suites. 79: [----------] Global test environment set-up. 79: [----------] 4 tests from InNvt/MultiSimTest 79: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Setting the LD random seed to -48276497 79: Setting the LD random seed to -1784872965 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Generating 1-4 interactions: fudge = 0.5 79: Setting the LD random seed to -546312210 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -838860830 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1460290837 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -538727633 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -688979969 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1687184394 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (221 ms) 79: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 79: Setting the LD random seed to -39878787 79: Setting the LD random seed to -596918323 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to 1492643571 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -69469207 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 32 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: NOTE: 33 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (117 ms) 79: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 3 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 0 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 1 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 2 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: Setting the LD random seed to -67371409 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -4674449 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -1109693284 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -748814342 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -1384122401 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -35395585 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to 2126494687 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1918389125 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (8 ms) 79: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -213918241 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1112145943 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -1090521219 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to 2079898103 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 0 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: NOTE: 23 % of the run time was spent in domain decomposition, 79: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 6 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 1 steps, 0.0 ps. 79: 79: Note: The number of steps is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: 79: NOTE: 34 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (14 ms) 79: [----------] 4 tests from InNvt/MultiSimTest (384 ms total) 79: 79: [----------] 2 tests from InNvt/MultiSimTerminationTest 79: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 12: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 11: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 11: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: Setting the LD random seed to -407515426 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1786773677 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -591401489 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -558235937 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -436209761 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -271601169 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to 2142762719 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -503435301 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Step 11: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: 79: NOTE: 10 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 14 steps, 0.0 ps (continuing from step 12, 0.0 ps). 79: 79: Note: The initial step is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: 79: NOTE: 18 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 79: 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 14 steps, 0.0 ps (continuing from step 12, 0.0 ps). 79: 79: Note: The initial step is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 15 steps, 0.0 ps (continuing from step 13, 0.0 ps). 79: 79: Note: The initial step is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 14 steps, 0.0 ps (continuing from step 12, 0.0 ps). 79: 79: Note: The initial step is not consistent across multi simulations, 79: but we are proceeding anyway! 79: 79: Writing final coordinates. 79: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (15 ms) 79: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 79: Setting the LD random seed to -1376291477 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -794757 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -68281973 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -30849 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group System is 9.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 7.8%. 79: The balanceable part of the MD step is 6%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: 79: NOTE: 27 % of the run time was spent in domain decomposition, 79: 8 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 23 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 37 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 100 steps, 0.1 ps. 79: 79: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 4.8%. 79: The balanceable part of the MD step is 7%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.3%. 79: 79: 79: NOTE: 26 % of the run time was spent in domain decomposition, 79: 8 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: NOTE: 23 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 79: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 79: 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: NOTE: 37 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (15 ms) 79: [----------] 2 tests from InNvt/MultiSimTerminationTest (36 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 6 tests from 2 test suites ran. (490 ms total) 79: [ PASSED ] 6 tests. 79/96 Test #79: MdrunMultiSimTests ........................... Passed 1.17 sec test 80 Start 80: MdrunMultiSimReplexTests 80: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 5 tests from 2 test suites. 80: [----------] Global test environment set-up. 80: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There were 2 NOTEs 80: Setting the LD random seed to -536928300 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -604377089 80: 80: Velocities were taken from a Maxwell distribution at 288 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -1120604330 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -553812513 80: 80: Velocities were taken from a Maxwell distribution at 278 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -1609881 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1857436647 80: 80: Velocities were taken from a Maxwell distribution at 298 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -1310720001 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 400432119 80: 80: Velocities were taken from a Maxwell distribution at 268 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 1 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 0 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 3 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: This is simulation 2 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (18 ms) 80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Setting the LD random seed to -537399339 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1222148365 80: 80: Velocities were taken from a Maxwell distribution at 288 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -318065739 80: Setting the LD random seed to 2134831039 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1844662887 80: 80: Velocities were taken from a Maxwell distribution at 298 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -138674337 80: 80: Velocities were taken from a Maxwell distribution at 278 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -608340353 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -562561590 80: 80: Velocities were taken from a Maxwell distribution at 268 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 2 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 3 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 0 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 1 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 0 out of 2 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.3%. 80: The balanceable part of the MD step is 11%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.0%. 80: 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 5 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 1 out of 2 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.8%. 80: The balanceable part of the MD step is 11%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.1%. 80: 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 5 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (15 ms) 80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 80: Setting the LD random seed to -25567234 80: Setting the LD random seed to -446039205 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -50335745 80: 80: Velocities were taken from a Maxwell distribution at 298 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (5 ms) 80: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -917514 80: 80: Velocities were taken from a Maxwell distribution at 278 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Setting the LD random seed to 1601566651 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 2145254069 80: 80: Velocities were taken from a Maxwell distribution at 278 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -34082889 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -587334661 80: 80: Velocities were taken from a Maxwell distribution at 298 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 1 out of 2 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.4%. 80: The balanceable part of the MD step is 12%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.1%. 80: 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 5 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: This is simulation 0 out of 2 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 2 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.0%. 80: The balanceable part of the MD step is 12%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.1%. 80: 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 4 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (38 ms) 80: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (78 ms total) 80: 80: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 80: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 80: Setting the LD random seed to -572262516 80: Setting the LD random seed to 1337375743 80: Setting the LD random seed to -269025505 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 80: 80: This is simulation 1 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 100 steps, 0.1 ps. 80: 80: Step 8: Run time exceeded 0.000 hours, will terminate the run within 400 steps 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 80: 80: This is simulation 0 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 100 steps, 0.1 ps. 80: 80: Step 8: Run time exceeded 0.000 hours, will terminate the run within 400 steps 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 80: 80: This is simulation 3 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 100 steps, 0.1 ps. 80: 80: Step 8: Run time exceeded 0.000 hours, will terminate the run within 400 steps 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 80: 80: This is simulation 2 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 100 steps, 0.1 ps. 80: 80: Step 8: Run time exceeded 0.000 hours, will terminate the run within 400 steps 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -621150466 80: 80: Velocities were taken from a Maxwell distribution at 288 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1996488063 80: 80: Velocities were taken from a Maxwell distribution at 298 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -422577187 80: 80: Velocities were taken from a Maxwell distribution at 278 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Setting the LD random seed to -776017026 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -409052161 80: 80: Velocities were taken from a Maxwell distribution at 268 K 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Writing final coordinates. 80: 80: Writing final coordinates. 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 80: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 80: 80: 80: This is simulation 2 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: 80: This is simulation 3 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 80: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 80: 80: 80: This is simulation 1 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 80: 80: Writing final coordinates. 80: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 80: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 80: 80: 80: This is simulation 0 out of 4 running as a composite GROMACS 80: multi-simulation job. Setup for this simulation: 80: 80: Using 1 MPI process 80: Using 1 OpenMP thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 80: 80: Writing final coordinates. 80: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (39 ms) 80: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (39 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 5 tests from 2 test suites ran. (181 ms total) 80: [ PASSED ] 5 tests. 80/96 Test #80: MdrunMultiSimReplexTests ..................... Passed 0.75 sec test 81 Start 81: MdrunMultiSimReplexEquivalenceTests 81: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 10 tests from 2 test suites. 81: [----------] Global test environment set-up. 81: [----------] 8 tests from LF/ReplicaExchangeTest 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 288 K 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 268 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 2 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 3 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 81: 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (339 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 288 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 268 K 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 3 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: This is simulation 1 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: This is simulation 2 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: This is simulation 0 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (284 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 268 K 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 288 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 3 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 2 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: .015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (234 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Velocities were taken from a Maxwell distribution at 288 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 268 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchanReading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: geTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 3 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 2 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (219 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.4%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.2%. 81: 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.2%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (185 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.0%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 14 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.6%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.7%. 81: 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (251 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.7%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.3%. 81: 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.4%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.7%. 81: 81: 81: NOTE: 13 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (234 ms) 81: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are generating velocities so I am assuming you are equilibrating a 81: system. You are using Parrinello-Rahman pressure coupling, but this can 81: be unstable for equilibration. If your system crashes, try equilibrating 81: first with Berendsen pressure coupling. If you are not equilibrating the 81: system, you can probably ignore this warning. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.9%. 81: The balanceable part of the MD step is 48%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.5%. 81: 81: 81: NOTE: 12 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.8%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 14 % of the run time was spent in domain decomposition, 81: 4 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 6 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (199 ms) 81: [----------] 8 tests from LF/ReplicaExchangeTest (1964 ms total) 81: 81: [----------] 2 tests from VV/ReplicaExchangeTest 81: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 288 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 268 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 1 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 2 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 3 out of 4 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Writing final coordinates. 81: 81: Writing final coordinates. 81: 81: Writing final coordinates. 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (282 ms) 81: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 81: You have set rlist larger than the interaction cut-off, but you also have 81: verlet-buffer-tolerance > 0. Will set rlist using 81: verlet-buffer-tolerance. 81: 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: Generating 1-4 interactions: fudge = 0.5 81: Generating 1-4 interactions: fudge = 0.5 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 298 K 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Velocities were taken from a Maxwell distribution at 278 K 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 81: 81: This is simulation 0 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: This is simulation 1 out of 2 running as a composite GROMACS 81: multi-simulation job. Setup for this simulation: 81: 81: Using 2 MPI processes 81: Using 1 OpenMP thread per MPI process 81: 81: Using 1 OpenMP thread per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.0%. 81: The balanceable part of the MD step is 1%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.0%. 81: 81: 81: NOTE: 39 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.3%. 81: The balanceable part of the MD step is 33%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 39 % of the run time was spent in domain decomposition, 81: 0 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (698 ms) 81: [----------] 2 tests from VV/ReplicaExchangeTest (998 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 10 tests from 2 test suites ran. (2999 ms total) 81: [ PASSED ] 10 tests. 81/96 Test #81: MdrunMultiSimReplexEquivalenceTests .......... Passed 3.73 sec test 82 Start 82: MdrunMpi1RankPmeTests 82: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 19 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 19 tests from ReproducesEnergies/PmeTest 82: Setting the LD random seed to 1920925159 82: 82: Generated 8 of the 10 non-bonded parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'Methanol' 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 82: Number of degrees of freedom in T-Coupling group rest is 12.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 82: NVE simulation: will use the initial temperature of 1046.791 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 82: For a correct single-point energy evaluation with nsteps = 0, use 82: continuation = yes to avoid constraining the input coordinates. 82: 82: Setting the LD random seed to 2069345147 82: 82: Generated 8 of the 10 non-bonded parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'Methanol' 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 82: 82: Searching the wall atom type(s) 82: Number of degrees of freedom in T-Coupling group rest is 13.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 82: NVE simulation: will use the initial temperature of 966.268 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 82: 82: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: Calculating fourier grid dimensions for X Y Z 82: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 82: 82: Estimate for the relative computational load of the PME mesh part: 1.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 82: The optimal PME mesh load for parallel simulations is below 0.5 82: and for highly parallel simulations between 0.25 and 0.33, 82: for higher performance, increase the cut-off and the PME grid spacing. 82: 82: 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 82: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc-and-methanol' 82: 20 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.009 199.0 82: (ns/day) (hour/ns) 82: Performance: 197.887 0.121 82: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 2 OpenMP threads 82: 82: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (9780 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc-and-methanol' 82: 20 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.415 0.208 200.0 82: (ns/day) (hour/ns) 82: Performance: 8.737 2.747 82: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 2 OpenMP threads 82: 82: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (225 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc-and-methanol' 82: 0 steps, 0.0 ps. 82: 82: NOTE: 30 % of the run time was spent in domain decomposition, 82: 10 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.4 82: (ns/day) (hour/ns) 82: Performance: 4.336 5.535 82: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 82: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 2 OpenMP threads 82: 82: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (30438 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets using PME rank(s) but the simulation is using only one rank 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc-and-methanol' 82: 20 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.415 0.207 200.0 82: (ns/day) (hour/ns) 82: Performance: 8.750 2.743 82: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (224 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 82: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 82: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 82: Test is being skipped because: 82: it targets GPU execution, but no compatible devices were detected 82: PME GPU does not support: 82: Non-GPU build of GROMACS. 82: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 82: [----------] 19 tests from ReproducesEnergies/PmeTest (40672 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 19 tests from 1 test suite ran. (40685 ms total) 82: [ PASSED ] 4 tests. 82: [ SKIPPED ] 15 tests, listed below: 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 82: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 82/96 Test #82: MdrunMpi1RankPmeTests ........................ Passed 41.07 sec test 83 Start 83: MdrunMpi2RankPmeTests 83: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 19 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 19 tests from ReproducesEnergies/PmeTest 83: Setting the LD random seed to -67244299 83: 83: Generated 8 of the 10 non-bonded parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'Methanol' 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 83: 83: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 1.00 83: 83: This run will generate roughly 0 Mb of data 83: Setting the LD random seed to -11657745 83: 83: Generated 8 of the 10 non-bonded parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'Methanol' 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc-and-methanol.gro' 83: 83: Searching the wall atom type(s) 83: 83: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 83: 83: Estimate for the relative computational load of the PME mesh part: 1.00 83: 83: This run will generate roughly 0 Mb of data 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 83: Number of degrees of freedom in T-Coupling group rest is 12.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 83: NVE simulation: will use the initial temperature of 1046.791 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There were 2 NOTEs 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 83: For a correct single-point energy evaluation with nsteps = 0, use 83: continuation = yes to avoid constraining the input coordinates. 83: 83: Number of degrees of freedom in T-Coupling group rest is 13.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 83: NVE simulation: will use the initial temperature of 966.268 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 9.4%. 83: The balanceable part of the MD step is 34%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 3.2%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.991 0.248 399.9 83: (ns/day) (hour/ns) 83: Performance: 7.321 3.278 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (12232 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 4.1%. 83: The balanceable part of the MD step is 29%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 5 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.107 0.277 399.9 83: (ns/day) (hour/ns) 83: Performance: 6.554 3.662 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (296 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 0 steps, 0.0 ps. 83: 83: NOTE: 32 % of the run time was spent in domain decomposition, 83: 10 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.270 0.068 399.4 83: (ns/day) (hour/ns) 83: Performance: 1.278 18.786 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (39562 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 83: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.542 0.386 399.8 83: (ns/day) (hour/ns) 83: Performance: 4.704 5.102 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (8349 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.018 0.255 399.7 83: (ns/day) (hour/ns) 83: Performance: 7.121 3.370 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (288 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 0 steps, 0.0 ps. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.029 0.008 367.4 83: (ns/day) (hour/ns) 83: Performance: 10.907 2.200 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (26830 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 83: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 2 OpenMP threads per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'spc-and-methanol' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 8.8%. 83: The balanceable part of the MD step is 32%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.8%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.068 0.267 399.9 83: (ns/day) (hour/ns) 83: Performance: 6.792 3.533 83: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (310 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 83: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 83: [----------] 19 tests from ReproducesEnergies/PmeTest (87896 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 19 tests from 1 test suite ran. (87924 ms total) 83: [ PASSED ] 7 tests. 83: [ SKIPPED ] 12 tests, listed below: 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 83: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 83/96 Test #83: MdrunMpi2RankPmeTests ........................ Passed 88.24 sec test 84 Start 84: MdrunCoordinationBasicTests1Rank 84: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 1 test from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 1 test from BasicPropagators/PeriodicActionsTest 84: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.002 89.0 84: (ns/day) (hour/ns) 84: Performance: 786.995 0.030 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.4 84: (ns/day) (hour/ns) 84: Performance: 2305.611 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (1). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2623.762 0.009 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: ng/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/TestiGenerated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (1). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.0 84: (ns/day) (hour/ns) 84: Performance: 2455.398 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (1). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.1 84: (ns/day) (hour/ns) 84: Performance: 2514.528 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (1). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 95.2 84: (ns/day) (hour/ns) 84: Performance: 2523.799 0.010 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (46 ms) 84: [----------] 1 test from BasicPropagators/PeriodicActionsTest (47 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 1 test from 1 test suite ran. (51 ms total) 84: [ PASSED ] 1 test. 84/96 Test #84: MdrunCoordinationBasicTests1Rank ............. Passed 0.31 sec test 85 Start 85: MdrunCoordinationBasicTests2Ranks 85: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 1 test from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 1 test from BasicPropagators/PeriodicActionsTest 85: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 38 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.004 0.002 195.1 85: (ns/day) (hour/ns) 85: Performance: 783.342 0.031 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 191.0 85: (ns/day) (hour/ns) 85: Performance: 1627.419 0.015 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (1). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.9%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.9%. 85: 85: 85: NOTE: 31 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 190.1 85: (ns/day) (hour/ns) 85: Performance: 1845.042 0.013 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (1). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 33.1%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 17.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 17.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.680 0.348 195.5 85: (ns/day) (hour/ns) 85: Performance: 4.221 5.685 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (1). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 33.1%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 16.3%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 16.3 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE: 12 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.648 0.332 195.3 85: (ns/day) (hour/ns) 85: Performance: 4.425 5.424 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (1). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.4%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: NOTE: 35 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.002 0.001 188.9 85: (ns/day) (hour/ns) 85: Performance: 1564.198 0.015 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1471 ms) 85: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1471 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 1 test from 1 test suite ran. (1477 ms total) 85: [ PASSED ] 1 test. 85/96 Test #85: MdrunCoordinationBasicTests2Ranks ............ Passed 1.84 sec test 86 Start 86: MdrunCoordinationCouplingTests1Rank 86: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 25 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 98.0 86: (ns/day) (hour/ns) 86: Performance: 859.938 0.028 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 2011.951 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2676.192 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2403.665 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2622.645 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2638.370 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (48 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1881.672 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 93.0 86: (ns/day) (hour/ns) 86: Performance: 1949.555 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2639.500 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2406.482 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2521.733 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2435.017 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (41 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1819.431 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2119.227 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2531.057 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2457.357 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2348.682 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (42 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2463.252 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1669.990 0.014 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2209.682 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2571.199 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2411.191 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2399.920 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2525.869 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (37 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.6 86: (ns/day) (hour/ns) 86: Performance: 1044.700 0.023 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2105.466 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2622.645 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2545.700 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2520.701 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2330.028 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (42 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1871.383 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2216.838 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2617.075 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.6 86: (ns/day) (hour/ns) 86: Performance: 2400.855 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2348.682 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2404.603 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (42 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1235.083 0.019 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2151.797 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.0 86: (ns/day) (hour/ns) 86: Performance: 2578.733 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2452.466 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.5 86: (ns/day) (hour/ns) 86: Performance: 2344.214 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2443.710 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (39 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1878.230 0.013 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1446.149 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2481.109 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2406.482 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1527.546 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2414.972 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (39 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1880.523 0.013 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1441.412 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2567.984 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2532.098 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2406.482 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2566.914 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (31 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1882.247 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2168.460 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 2612.635 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.7 86: (ns/day) (hour/ns) 86: Performance: 2455.398 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2432.133 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2347.787 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (31 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1940.956 0.012 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2142.815 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 91.1 86: (ns/day) (hour/ns) 86: Performance: 2564.777 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriGenerated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: odicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.2 86: (ns/day) (hour/ns) 86: Performance: 2461.284 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2486.115 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2520.701 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (30 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1290.447 0.019 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 2102.592 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2535.224 0.009 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.9 86: (ns/day) (hour/ns) 86: Performance: 2525.869 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2450.515 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 94.8 86: (ns/day) (hour/ns) 86: Performance: 2505.325 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (35 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.8 86: (ns/day) (hour/ns) 86: Performance: 1980.262 0.012 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.4 86: (ns/day) (hour/ns) 86: Performance: 2204.148 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.8 86: (ns/day) (hour/ns) 86: Performance: 1617.378 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2512.477 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.1 86: (ns/day) (hour/ns) 86: Performance: 2511.453 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.4 86: (ns/day) (hour/ns) 86: Performance: 2477.119 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (34 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1810.874 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 2008.016 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2337.099 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2382.287 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1246.327 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2354.967 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (35 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1834.056 0.013 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 49.8 86: (ns/day) (hour/ns) 86: Performance: 1027.108 0.023 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 2466.210 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2324.752 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.3 86: (ns/day) (hour/ns) 86: Performance: 2348.682 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.7 86: (ns/day) (hour/ns) 86: Performance: 2408.363 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (35 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1815.677 0.013 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1827.527 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2322.124 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.5 86: (ns/day) (hour/ns) 86: Performance: 2337.099 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 2274.121 0.011 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.6 86: (ns/day) (hour/ns) 86: Performance: 2414.972 0.010 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (40 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 98.3 86: (ns/day) (hour/ns) 86: Performance: 882.860 0.027 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1769.269 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1974.549 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 98.1 86: (ns/day) (hour/ns) 86: Performance: 1060.526 0.023 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1888.015 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1906.124 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (31 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 98.3 86: (ns/day) (hour/ns) 86: Performance: 928.779 0.026 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1662.778 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1237.315 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.4 86: (ns/day) (hour/ns) 86: Performance: 1721.317 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1742.249 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 98.0 86: (ns/day) (hour/ns) 86: Performance: 988.542 0.024 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (33 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.7 86: (ns/day) (hour/ns) 86: Performance: 1435.367 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1642.387 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.1 86: (ns/day) (hour/ns) 86: Performance: 1758.662 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1720.356 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.5 86: (ns/day) (hour/ns) 86: Performance: 1750.169 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1703.704 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (33 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1473.474 0.016 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.1 86: (ns/day) (hour/ns) 86: Performance: 1249.613 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.9 86: (ns/day) (hour/ns) 86: Performance: 1944.018 0.012 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1270.226 0.019 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.0 86: (ns/day) (hour/ns) 86: Performance: 1813.006 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1825.902 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (32 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1422.770 0.017 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1589.831 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 95.8 86: (ns/day) (hour/ns) 86: Performance: 1809.279 0.013 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.3 86: (ns/day) (hour/ns) 86: Performance: 1212.000 0.020 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1736.357 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.3 86: (ns/day) (hour/ns) 86: Performance: 1728.562 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (33 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1398.228 0.017 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1607.671 0.015 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 72.9 86: (ns/day) (hour/ns) 86: Performance: 1304.934 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1736.846 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1707.955 0.014 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1080.616 0.022 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (32 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.0 86: (ns/day) (hour/ns) 86: Performance: 1260.351 0.019 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1362.360 0.018 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.2 86: (ns/day) (hour/ns) 86: Performance: 1484.838 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.003 0.003 98.5 86: (ns/day) (hour/ns) 86: Performance: 500.780 0.048 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1456.750 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1469.958 0.016 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (37 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 97.5 86: (ns/day) (hour/ns) 86: Performance: 719.611 0.033 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 4 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.9 86: (ns/day) (hour/ns) 86: Performance: 1090.950 0.022 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 97.5 86: (ns/day) (hour/ns) 86: Performance: 801.534 0.030 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.9 86: (ns/day) (hour/ns) 86: Performance: 1149.579 0.021 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.002 0.002 97.5 86: (ns/day) (hour/ns) 86: Performance: 782.496 0.031 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: MTTK coupling is deprecated and will soon be removed 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: for current Trotter decomposition methods with vv, nsttcouple and 86: nstpcouple must be equal. Both have been reset to 86: min(nsttcouple,nstpcouple) = 2 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 5 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1124.196 0.021 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (37 ms) 86: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 97.2 86: (ns/day) (hour/ns) 86: Performance: 1177.034 0.020 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.6 86: (ns/day) (hour/ns) 86: Performance: 1303.829 0.018 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.1 86: (ns/day) (hour/ns) 86: Performance: 1430.368 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.7 86: (ns/day) (hour/ns) 86: Performance: 1417.206 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.002 58.8 86: (ns/day) (hour/ns) 86: Performance: 826.592 0.029 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.001 0.001 96.5 86: (ns/day) (hour/ns) 86: Performance: 1387.521 0.017 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 86: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (34 ms) 86: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (921 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 25 tests from 1 test suite ran. (925 ms total) 86: [ PASSED ] 25 tests. 86/96 Test #86: MdrunCoordinationCouplingTests1Rank .......... Passed 1.25 sec test 87 Start 87: MdrunCoordinationCouplingTests2Ranks 87: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 25 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 194.9 87: (ns/day) (hour/ns) 87: Performance: 720.579 0.033 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.7%. 87: The balanceable part of the MD step is 49%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1560.236 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.9%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.1%. 87: 87: 87: NOTE: 13 % of the run time was spent in domain decomposition, 87: 4 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.8 87: (ns/day) (hour/ns) 87: Performance: 1667.053 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActioOpened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 nsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.4%. 87: The balanceable part of the MD step is 35%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.2%. 87: 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1735.379 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.7%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.4%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 178.9 87: (ns/day) (hour/ns) 87: Performance: 1624.629 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.6%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.3%. 87: 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1639.982 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (97 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.5 87: (ns/day) (hour/ns) 87: Performance: 1345.255 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.9%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.5 87: (ns/day) (hour/ns) 87: Performance: 1443.607 0.017 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReOpened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 ference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1710.801 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 19%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 38 % of the run time was spent in domain decomposition, 87: 3 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 192.9 87: (ns/day) (hour/ns) 87: Performance: 1080.901 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.5%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.7 87: (ns/day) (hour/ns) 87: Performance: 1621.636 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1632.810 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (56 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.2 87: (ns/day) (hour/ns) 87: Performance: 1317.211 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: NOTE: 91 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.018 0.009 196.8 87: (ns/day) (hour/ns) 87: Performance: 164.876 0.146 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.5%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.1%. 87: 87: 87: NOTE: 86 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 194.4 87: (ns/day) (hour/ns) 87: Performance: 294.638 0.081 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 4 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1493.477 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1606.832 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1636.280 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (87 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.7 87: (ns/day) (hour/ns) 87: Performance: 1270.226 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 4%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.0%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.018 0.009 198.9 87: (ns/day) (hour/ns) 87: Performance: 159.866 0.150 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.9%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.2%. 87: 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1650.970 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 1574.794 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 88 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 194.3 87: (ns/day) (hour/ns) 87: Performance: 289.175 0.083 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 43%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1534.968 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (74 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 199.2 87: (ns/day) (hour/ns) 87: Performance: 110.825 0.217 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1638.020 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.0 87: (ns/day) (hour/ns) 87: Performance: 1950.172 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 187.5 87: (ns/day) (hour/ns) 87: Performance: 1837.064 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1845.042 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.8 87: (ns/day) (hour/ns) 87: Performance: 1819.700 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (88 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.6 87: (ns/day) (hour/ns) 87: Performance: 1461.588 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1616.105 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 187.8 87: (ns/day) (hour/ns) 87: Performance: 1839.532 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.7 87: (ns/day) (hour/ns) 87: Performance: 1218.954 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.3 87: (ns/day) (hour/ns) 87: Performance: 1739.298 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 1710.563 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (60 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 1440.906 0.017 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1625.272 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1875.086 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.1 87: (ns/day) (hour/ns) 87: Performance: 1746.943 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 197.7 87: (ns/day) (hour/ns) 87: Performance: 278.861 0.086 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.1 87: (ns/day) (hour/ns) 87: Performance: 1663.227 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (70 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.7 87: (ns/day) (hour/ns) 87: Performance: 1343.934 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.5 87: (ns/day) (hour/ns) 87: Performance: 1589.626 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.8 87: (ns/day) (hour/ns) 87: Performance: 1808.747 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.1 87: (ns/day) (hour/ns) 87: Performance: 1704.647 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 1725.173 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1522.638 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (65 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.5 87: (ns/day) (hour/ns) 87: Performance: 1466.633 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.018 0.009 198.9 87: (ns/day) (hour/ns) 87: Performance: 160.560 0.149 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1993.397 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1781.806 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.4 87: (ns/day) (hour/ns) 87: Performance: 1790.350 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.4 87: (ns/day) (hour/ns) 87: Performance: 1140.428 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (96 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 190.4 87: (ns/day) (hour/ns) 87: Performance: 1095.606 0.022 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 1606.413 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 58 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 192.2 87: (ns/day) (hour/ns) 87: Performance: 1052.104 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1699.005 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1748.678 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (46 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1750.417 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.2 87: (ns/day) (hour/ns) 87: Performance: 1369.477 0.018 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1318.197 0.018 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.4 87: (ns/day) (hour/ns) 87: Performance: 1804.509 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.2 87: (ns/day) (hour/ns) 87: Performance: 1455.545 0.016 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 1818.357 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 86 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.009 0.005 197.1 87: (ns/day) (hour/ns) 87: Performance: 306.871 0.078 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 3 NOTEs 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (40 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.1 87: (ns/day) (hour/ns) 87: Performance: 1270.618 0.019 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1571.781 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.0 87: (ns/day) (hour/ns) 87: Performance: 1802.661 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 35 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1650.085 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.4 87: (ns/day) (hour/ns) 87: Performance: 1795.045 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 36 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.1 87: (ns/day) (hour/ns) 87: Performance: 1774.365 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (54 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.4 87: (ns/day) (hour/ns) 87: Performance: 1500.936 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 199.2 87: (ns/day) (hour/ns) 87: Performance: 112.170 0.214 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 3 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 2002.468 0.012 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 3 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1823.200 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 3 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 33 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1878.803 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1902.005 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (59 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.1 87: (ns/day) (hour/ns) 87: Performance: 1464.716 0.016 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.1 87: (ns/day) (hour/ns) 87: Performance: 1605.157 0.015 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 198.1 87: (ns/day) (hour/ns) 87: Performance: 289.182 0.083 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 1769.777 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.3 87: (ns/day) (hour/ns) 87: Performance: 1765.719 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 1736.112 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (68 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 198.0 87: (ns/day) (hour/ns) 87: Performance: 278.093 0.086 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.4 87: (ns/day) (hour/ns) 87: Performance: 1662.778 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.6 87: (ns/day) (hour/ns) 87: Performance: 1850.306 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.010 0.005 198.0 87: (ns/day) (hour/ns) 87: Performance: 295.905 0.081 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 1790.350 0.013 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 1728.077 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (55 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 191.6 87: (ns/day) (hour/ns) 87: Performance: 1441.075 0.017 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE: 92 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.017 0.009 198.1 87: (ns/day) (hour/ns) 87: Performance: 168.127 0.143 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1777.180 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1694.333 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1773.088 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.9 87: (ns/day) (hour/ns) 87: Performance: 1655.184 0.014 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (64 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 6 % of the run time was spent in domain decomposition, 87: 12 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 19 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 191.2 87: (ns/day) (hour/ns) 87: Performance: 772.779 0.031 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 60%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 184.4 87: (ns/day) (hour/ns) 87: Performance: 1053.183 0.023 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 47%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.1 87: (ns/day) (hour/ns) 87: Performance: 1223.554 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.7%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.2%. 87: 87: 87: NOTE: 25 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 185.7 87: (ns/day) (hour/ns) 87: Performance: 1196.929 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.2%. 87: The balanceable part of the MD step is 21%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 16 % of the run time was spent in domain decomposition, 87: 3 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 19 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 189.3 87: (ns/day) (hour/ns) 87: Performance: 911.465 0.026 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.6%. 87: The balanceable part of the MD step is 45%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.6%. 87: 87: 87: NOTE: 23 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 172.6 87: (ns/day) (hour/ns) 87: Performance: 1084.707 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (41 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 37 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 189.1 87: (ns/day) (hour/ns) 87: Performance: 653.852 0.037 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.3%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 1017.355 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 54%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.4 87: (ns/day) (hour/ns) 87: Performance: 1086.141 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.4%. 87: The balanceable part of the MD step is 30%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.1%. 87: 87: 87: NOTE: 6 % of the run time was spent in domain decomposition, 87: 15 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 188.9 87: (ns/day) (hour/ns) 87: Performance: 772.004 0.031 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.7 87: (ns/day) (hour/ns) 87: Performance: 1075.241 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.2 87: (ns/day) (hour/ns) 87: Performance: 966.747 0.025 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (41 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 190.3 87: (ns/day) (hour/ns) 87: Performance: 726.571 0.033 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: There were 3 NOTEs 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 58%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.2 87: (ns/day) (hour/ns) 87: Performance: 989.097 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 54%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.0 87: (ns/day) (hour/ns) 87: Performance: 1098.929 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 32 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 188.4 87: (ns/day) (hour/ns) 87: Performance: 807.629 0.030 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: There were 3 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 52%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.2 87: (ns/day) (hour/ns) 87: Performance: 1049.952 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 87: NVE simulation: will use the initial temperature of 68.810 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 53%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.6 87: (ns/day) (hour/ns) 87: Performance: 1040.465 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (39 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 190.8 87: (ns/day) (hour/ns) 87: Performance: 667.743 0.036 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.5 87: (ns/day) (hour/ns) 87: Performance: 1067.601 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 185.0 87: (ns/day) (hour/ns) 87: Performance: 1192.411 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: COM rOpened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 emoval frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 184.0 87: (ns/day) (hour/ns) 87: Performance: 1191.719 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 180.5 87: (ns/day) (hour/ns) 87: Performance: 1176.359 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 183.7 87: (ns/day) (hour/ns) 87: Performance: 1210.452 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (43 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 6 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 189.8 87: (ns/day) (hour/ns) 87: Performance: 678.853 0.035 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.0 87: (ns/day) (hour/ns) 87: Performance: 1106.727 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 184.5 87: (ns/day) (hour/ns) 87: Performance: 1179.174 0.020 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 185.6 87: (ns/day) (hour/ns) 87: Performance: 798.729 0.030 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 183.7 87: (ns/day) (hour/ns) 87: Performance: 1106.528 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: 87: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 87: The Berendsen barostat does not generate any strictly correct ensemble, 87: and should not be used for new production simulations (in our opinion). 87: We recommend using the C-rescale barostat instead. 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: 87: There was 1 WARNING 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 18 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.9 87: (ns/day) (hour/ns) 87: Performance: 811.566 0.030 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (39 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 166.8 87: (ns/day) (hour/ns) 87: Performance: 751.567 0.032 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.6 87: (ns/day) (hour/ns) 87: Performance: 1086.812 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 184.8 87: (ns/day) (hour/ns) 87: Performance: 1161.828 0.021 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 17 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 185.8 87: (ns/day) (hour/ns) 87: Performance: 841.094 0.029 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 184.8 87: (ns/day) (hour/ns) 87: Performance: 1076.839 0.022 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.1 87: (ns/day) (hour/ns) 87: Performance: 919.903 0.026 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (39 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.0 87: (ns/day) (hour/ns) 87: Performance: 884.380 0.027 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.5 87: (ns/day) (hour/ns) 87: Performance: 974.315 0.025 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.4 87: (ns/day) (hour/ns) 87: Performance: 1034.525 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.9 87: (ns/day) (hour/ns) 87: Performance: 1013.006 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.0 87: (ns/day) (hour/ns) 87: Performance: 977.794 0.025 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 3 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 185.7 87: (ns/day) (hour/ns) 87: Performance: 995.812 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (44 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 188.4 87: (ns/day) (hour/ns) 87: Performance: 747.872 0.032 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 188.5 87: (ns/day) (hour/ns) 87: Performance: 706.490 0.034 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.8 87: (ns/day) (hour/ns) 87: Performance: 863.978 0.028 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.5 87: (ns/day) (hour/ns) 87: Performance: 852.854 0.028 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.7 87: (ns/day) (hour/ns) 87: Performance: 796.920 0.030 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: MTTK coupling is deprecated and will soon be removed 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: for current Trotter decomposition methods with vv, nsttcouple and 87: nstpcouple must be equal. Both have been reset to 87: min(nsttcouple,nstpcouple) = 2 87: 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 7 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.9 87: (ns/day) (hour/ns) 87: Performance: 844.206 0.028 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (56 ms) 87: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 153.9 87: (ns/day) (hour/ns) 87: Performance: 704.833 0.034 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 19 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.004 0.002 189.8 87: (ns/day) (hour/ns) 87: Performance: 669.739 0.036 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.9 87: (ns/day) (hour/ns) 87: Performance: 1043.284 0.023 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.001 186.1 87: (ns/day) (hour/ns) 87: Performance: 985.380 0.024 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 186.4 87: (ns/day) (hour/ns) 87: Performance: 957.432 0.025 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'Argon' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon12.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (50 ms) 87: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (1488 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 25 tests from 1 test suite ran. (1508 ms total) 87: [ PASSED ] 25 tests. 87: Number of degrees of freedom in T-Coupling group System is 33.00 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Argon' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: NOTE: 8 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 187.3 87: (ns/day) (hour/ns) 87: Performance: 906.703 0.026 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 87/96 Test #87: MdrunCoordinationCouplingTests2Ranks ......... Passed 1.80 sec test 88 Start 88: MdrunCoordinationConstraintsTests1Rank 88: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 88: Test timeout computed to be: 1920 88: [==========] Running 13 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 1765.719 0.014 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.1 88: (ns/day) (hour/ns) 88: Performance: 1864.022 0.013 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 4. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 4. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.6 88: (ns/day) (hour/ns) 88: Performance: 2360.381 0.010 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.4 88: (ns/day) (hour/ns) 88: Performance: 2147.297 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.6 88: (ns/day) (hour/ns) 88: Performance: 2121.417 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2168.460 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1089 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.7 88: (ns/day) (hour/ns) 88: Performance: 1686.448 0.014 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 1208.433 0.020 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.4 88: (ns/day) (hour/ns) 88: Performance: 1722.761 0.014 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2043.993 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.005 14.7 88: (ns/day) (hour/ns) 88: Performance: 301.163 0.080 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.4 88: (ns/day) (hour/ns) 88: Performance: 1984.088 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1274 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.5 88: (ns/day) (hour/ns) 88: Performance: 1137.270 0.021 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.2 88: (ns/day) (hour/ns) 88: Performance: 1877.657 0.013 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.9 88: (ns/day) (hour/ns) 88: Performance: 1493.115 0.016 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2084.098 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.9 88: (ns/day) (hour/ns) 88: Performance: 1942.792 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 1424.744 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1054 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 1756.156 0.014 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.1 88: (ns/day) (hour/ns) 88: Performance: 1968.241 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2304.749 0.010 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.8 88: (ns/day) (hour/ns) 88: Performance: 2104.747 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.7 88: (ns/day) (hour/ns) 88: Performance: 2145.054 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2119.957 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (964 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.6 88: (ns/day) (hour/ns) 88: Performance: 1193.451 0.020 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.6 88: (ns/day) (hour/ns) 88: Performance: 1956.365 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.3 88: (ns/day) (hour/ns) 88: Performance: 2376.772 0.010 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 1525.655 0.016 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.5 88: (ns/day) (hour/ns) 88: Performance: 1008.776 0.024 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: NOTE: 30 % of the run time was spent in pair search, 88: you might want to increase nstlist (this has no effect on accuracy) 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 1417.206 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1019 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.2 88: (ns/day) (hour/ns) 88: Performance: 1665.475 0.014 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 1878.230 0.013 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.2 88: (ns/day) (hour/ns) 88: Performance: 2101.157 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.5 88: (ns/day) (hour/ns) 88: Performance: 2167.697 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.2 88: (ns/day) (hour/ns) 88: Performance: 2157.826 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 94.9 88: (ns/day) (hour/ns) 88: Performance: 2196.290 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (972 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.7 88: (ns/day) (hour/ns) 88: Performance: 1667.730 0.014 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.2 88: (ns/day) (hour/ns) 88: Performance: 1967.612 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 4. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 4. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.5 88: (ns/day) (hour/ns) 88: Performance: 2206.516 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 2111.238 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 2101.874 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.5 88: (ns/day) (hour/ns) 88: Performance: 2050.114 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (961 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.9 88: (ns/day) (hour/ns) 88: Performance: 1349.823 0.018 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: 88: There were 3 NOTEs 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.5 88: (ns/day) (hour/ns) 88: Performance: 1414.927 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.3 88: (ns/day) (hour/ns) 88: Performance: 2145.054 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.7 88: (ns/day) (hour/ns) 88: Performance: 1955.744 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 2084.803 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.4 88: (ns/day) (hour/ns) 88: Performance: 2013.924 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (990 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.3 88: (ns/day) (hour/ns) 88: Performance: 1591.885 0.015 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.6 88: (ns/day) (hour/ns) 88: Performance: 1813.006 0.013 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.5 88: (ns/day) (hour/ns) 88: Performance: 2161.612 0.011 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.3 88: (ns/day) (hour/ns) 88: Performance: 2002.794 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.6 88: (ns/day) (hour/ns) 88: Performance: 2059.710 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.4 88: (ns/day) (hour/ns) 88: Performance: 1972.021 0.012 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (968 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.6 88: (ns/day) (hour/ns) 88: Performance: 1307.149 0.018 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.1 88: (ns/day) (hour/ns) 88: Performance: 1288.558 0.019 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 4. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 4. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.2 88: (ns/day) (hour/ns) 88: Performance: 1455.717 0.016 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.7 88: (ns/day) (hour/ns) 88: Performance: 1556.492 0.015 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.1 88: (ns/day) (hour/ns) 88: Performance: 1590.241 0.015 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 100. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 100. 88: 88: 88: There were 5 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.3 88: (ns/day) (hour/ns) 88: Performance: 1521.886 0.016 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (995 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.002 0.002 97.9 88: (ns/day) (hour/ns) 88: Performance: 920.178 0.026 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.2 88: (ns/day) (hour/ns) 88: Performance: 1374.519 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.1 88: (ns/day) (hour/ns) 88: Performance: 1563.999 0.015 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.2 88: (ns/day) (hour/ns) 88: Performance: 1329.720 0.018 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 4 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.8 88: (ns/day) (hour/ns) 88: Performance: 1368.109 0.018 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: NVE simulation: will use the initial temperature of 398.997 K for 88: determining the Verlet buffer size 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 97.0 88: (ns/day) (hour/ns) 88: Performance: 1421.785 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1122 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.008 0.008 99.4 88: (ns/day) (hour/ns) 88: Performance: 177.851 0.135 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.2 88: (ns/day) (hour/ns) 88: Performance: 1412.332 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.1 88: (ns/day) (hour/ns) 88: Performance: 1629.787 0.015 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.9 88: (ns/day) (hour/ns) 88: Performance: 1178.610 0.020 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.3 88: (ns/day) (hour/ns) 88: Performance: 1508.840 0.016 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 88: COM removal frequency is set to (5). 88: Other settings require a global communication frequency of 2. 88: Note that this will require additional global communication steps, 88: which will reduce performance when using multiple ranks. 88: Consider setting nstcomm to a multiple of 2. 88: 88: 88: There were 4 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.1 88: (ns/day) (hour/ns) 88: Performance: 1432.363 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1173 ms) 88: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.7 88: (ns/day) (hour/ns) 88: Performance: 1221.855 0.020 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (1) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.8 88: (ns/day) (hour/ns) 88: Performance: 1048.969 0.023 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: Setting nstcalcenergy (100) equal to nstenergy (4) 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 1429.704 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: This run will generate roughly 0 Mb of data 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 95.8 88: (ns/day) (hour/ns) 88: Performance: 1356.361 0.018 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.0 88: (ns/day) (hour/ns) 88: Performance: 1413.304 0.017 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 88: setting nstcomm equal to nstcalcenergy for less overhead 88: 88: Generated 330891 of the 330891 non-bonded parameter combinations 88: Generating 1-4 interactions: fudge = 0.5 88: 88: Generated 330891 of the 330891 1-4 parameter combinations 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: Number of degrees of freedom in T-Coupling group System is 27.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 3 NOTEs 88: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 88: 88: Using 1 MPI process 88: Using 1 OpenMP thread 88: 88: 88: NOTE: Thread affinity was not set. 88: starting mdrun 'spc2' 88: 16 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.001 0.001 96.3 88: (ns/day) (hour/ns) 88: Performance: 1360.255 0.018 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 88: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 88: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (998 ms) 88: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (13589 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 13 tests from 1 test suite ran. (13593 ms total) 88: [ PASSED ] 13 tests. 88/96 Test #88: MdrunCoordinationConstraintsTests1Rank ....... Passed 13.87 sec test 89 Start 89: MdrunCoordinationConstraintsTests2Ranks 89: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 89: Test timeout computed to be: 1920 89: [==========] Running 13 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 51%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.7%. 89: 89: 89: NOTE: 26 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.1 89: (ns/day) (hour/ns) 89: Performance: 1266.179 0.019 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 49%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: NOTE: 10 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 28 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.0 89: (ns/day) (hour/ns) 89: Performance: 1453.827 0.017 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 4. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 4. 89: 89: 89: There were 5 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 39%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 11 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 27 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.4 89: (ns/day) (hour/ns) 89: Performance: 1726.382 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 2.9%. 89: The balanceable part of the MD step is 38%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 1.1%. 89: 89: 89: NOTE: 11 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 28 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.3 89: (ns/day) (hour/ns) 89: Performance: 1726.866 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 38%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 11 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 28 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.3 89: (ns/day) (hour/ns) 89: Performance: 1709.140 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.8%. 89: The balanceable part of the MD step is 38%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.7%. 89: 89: 89: NOTE: 10 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 28 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.1 89: (ns/day) (hour/ns) 89: Performance: 1693.867 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1341 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 52%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.7%. 89: 89: 89: NOTE: 25 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.1 89: (ns/day) (hour/ns) 89: Performance: 1271.405 0.019 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.5%. 89: The balanceable part of the MD step is 50%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.8%. 89: 89: 89: NOTE: 10 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 26 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.9 89: (ns/day) (hour/ns) 89: Performance: 1501.851 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.3%. 89: The balanceable part of the MD step is 44%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: NOTE: 11 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 28 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.4 89: (ns/day) (hour/ns) 89: Performance: 1634.543 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.7%. 89: The balanceable part of the MD step is 42%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.3%. 89: 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.3 89: (ns/day) (hour/ns) 89: Performance: 1509.210 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.9%. 89: The balanceable part of the MD step is 43%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.4%. 89: 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 185.8 89: (ns/day) (hour/ns) 89: Performance: 1522.826 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.3%. 89: The balanceable part of the MD step is 44%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.0 89: (ns/day) (hour/ns) 89: Performance: 1603.695 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1509 ms) 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 53%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: NOTE: 39 % of the run time was spent in domain decomposition, 89: 1 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.011 0.006 198.0 89: (ns/day) (hour/ns) 89: Performance: 260.777 0.092 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.8%. 89: The balanceable part of the MD step is 49%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.4%. 89: 89: 89: NOTE: 47 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.019 0.009 198.6 89: (ns/day) (hour/ns) 89: Performance: 155.848 0.154 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.5%. 89: The balanceable part of the MD step is 6%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.0%. 89: 89: 89: NOTE: 15 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 197.8 89: (ns/day) (hour/ns) 89: Performance: 280.838 0.085 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.2%. 89: The balanceable part of the MD step is 37%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.4%. 89: 89: 89: NOTE: 13 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.8 89: (ns/day) (hour/ns) 89: Performance: 1376.515 0.017 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 43%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 10 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.3 89: (ns/day) (hour/ns) 89: Performance: 1546.140 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.6%. 89: The balanceable part of the MD step is 43%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.3%. 89: 89: 89: NOTE: 10 % of the run time was spent in domain decomposition, 89: 5 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.1 89: (ns/day) (hour/ns) 89: Performance: 1574.593 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1454 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.1 89: (ns/day) (hour/ns) 89: Performance: 1351.897 0.018 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 41 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.010 0.005 198.0 89: (ns/day) (hour/ns) 89: Performance: 279.012 0.086 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.3 89: (ns/day) (hour/ns) 89: Performance: 1840.907 0.013 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.8 89: (ns/day) (hour/ns) 89: Performance: 1734.646 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 183.8 89: (ns/day) (hour/ns) 89: Performance: 1651.191 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.4 89: (ns/day) (hour/ns) 89: Performance: 1696.432 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1550 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.011 0.005 197.6 89: (ns/day) (hour/ns) 89: Performance: 269.268 0.089 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.2 89: (ns/day) (hour/ns) 89: Performance: 1553.352 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.2 89: (ns/day) (hour/ns) 89: Performance: 1779.747 0.013 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.6 89: (ns/day) (hour/ns) 89: Performance: 1695.732 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.1 89: (ns/day) (hour/ns) 89: Performance: 1669.990 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.8 89: (ns/day) (hour/ns) 89: Performance: 1548.277 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1205 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.1 89: (ns/day) (hour/ns) 89: Performance: 1297.104 0.019 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.6 89: (ns/day) (hour/ns) 89: Performance: 1475.945 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.5 89: (ns/day) (hour/ns) 89: Performance: 1655.406 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.1 89: (ns/day) (hour/ns) 89: Performance: 1648.981 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.2 89: (ns/day) (hour/ns) 89: Performance: 1617.166 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.0 89: (ns/day) (hour/ns) 89: Performance: 1636.715 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1039 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.4 89: (ns/day) (hour/ns) 89: Performance: 1333.029 0.018 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.2 89: (ns/day) (hour/ns) 89: Performance: 1502.950 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 4. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 4. 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.4 89: (ns/day) (hour/ns) 89: Performance: 1481.981 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 4 NOTEs 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.9 89: (ns/day) (hour/ns) 89: Performance: 1457.784 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.004 0.002 195.3 89: (ns/day) (hour/ns) 89: Performance: 750.514 0.032 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.7 89: (ns/day) (hour/ns) 89: Performance: 1662.330 0.014 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (971 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.5 89: (ns/day) (hour/ns) 89: Performance: 1300.801 0.018 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 5 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 191.8 89: (ns/day) (hour/ns) 89: Performance: 1035.307 0.023 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 191.0 89: (ns/day) (hour/ns) 89: Performance: 1440.906 0.017 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.0 89: (ns/day) (hour/ns) 89: Performance: 1558.460 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 14 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 192.0 89: (ns/day) (hour/ns) 89: Performance: 1214.030 0.020 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.2 89: (ns/day) (hour/ns) 89: Performance: 1584.922 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (961 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 25 % of the run time was spent in domain decomposition, 89: 2 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 193.4 89: (ns/day) (hour/ns) 89: Performance: 924.181 0.026 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.4 89: (ns/day) (hour/ns) 89: Performance: 1464.541 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 12 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.2 89: (ns/day) (hour/ns) 89: Performance: 1514.962 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.1 89: (ns/day) (hour/ns) 89: Performance: 1567.382 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.9 89: (ns/day) (hour/ns) 89: Performance: 1554.332 0.015 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 190.0 89: (ns/day) (hour/ns) 89: Performance: 1539.956 0.016 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1020 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.2%. 89: The balanceable part of the MD step is 58%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.1%. 89: 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.004 0.002 189.8 89: (ns/day) (hour/ns) 89: Performance: 777.313 0.031 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.6%. 89: The balanceable part of the MD step is 59%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.4%. 89: 89: 89: NOTE: 9 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 188.3 89: (ns/day) (hour/ns) 89: Performance: 1009.189 0.024 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 4. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 4. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 49%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 186.7 89: (ns/day) (hour/ns) 89: Performance: 1125.428 0.021 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 46%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 185.4 89: (ns/day) (hour/ns) 89: Performance: 1076.086 0.022 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 46%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.7%. 89: 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 185.9 89: (ns/day) (hour/ns) 89: Performance: 1079.008 0.022 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 100. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 100. 89: 89: 89: There were 5 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.3%. 89: The balanceable part of the MD step is 46%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 186.6 89: (ns/day) (hour/ns) 89: Performance: 1121.637 0.021 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1020 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.3%. 89: The balanceable part of the MD step is 59%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.2%. 89: 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 188.5 89: (ns/day) (hour/ns) 89: Performance: 866.530 0.028 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.7%. 89: The balanceable part of the MD step is 57%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.4%. 89: 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 188.6 89: (ns/day) (hour/ns) 89: Performance: 931.941 0.026 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 0.9%. 89: The balanceable part of the MD step is 53%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 187.4 89: (ns/day) (hour/ns) 89: Performance: 932.152 0.026 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.0%. 89: The balanceable part of the MD step is 55%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.5%. 89: 89: 89: NOTE: 9 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 186.9 89: (ns/day) (hour/ns) 89: Performance: 988.383 0.024 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.1%. 89: The balanceable part of the MD step is 53%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.6%. 89: 89: 89: NOTE: 9 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 187.4 89: (ns/day) (hour/ns) 89: Performance: 996.376 0.024 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 1.4%. 89: The balanceable part of the MD step is 54%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.7%. 89: 89: 89: NOTE: 9 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 187.0 89: (ns/day) (hour/ns) 89: Performance: 1000.015 0.024 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1319 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 186.1 89: (ns/day) (hour/ns) 89: Performance: 911.128 0.026 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 186.6 89: (ns/day) (hour/ns) 89: Performance: 965.913 0.025 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 185.0 89: (ns/day) (hour/ns) 89: Performance: 1113.830 0.022 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.004 0.002 188.7 89: (ns/day) (hour/ns) 89: Performance: 717.851 0.033 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 184.7 89: (ns/day) (hour/ns) 89: Performance: 1109.817 0.022 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 89: COM removal frequency is set to (5). 89: Other settings require a global communication frequency of 2. 89: Note that this will require additional global communication steps, 89: which will reduce performance when using multiple ranks. 89: Consider setting nstcomm to a multiple of 2. 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 186.4 89: (ns/day) (hour/ns) 89: Performance: 843.455 0.028 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1093 ms) 89: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 6 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.004 0.002 188.5 89: (ns/day) (hour/ns) 89: Performance: 736.957 0.033 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (1) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 8 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 185.8 89: (ns/day) (hour/ns) 89: Performance: 1000.340 0.024 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 13 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 188.0 89: (ns/day) (hour/ns) 89: Performance: 853.150 0.028 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.002 179.0 89: (ns/day) (hour/ns) 89: Performance: 965.383 0.025 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 184.6 89: (ns/day) (hour/ns) 89: Performance: 1030.200 0.023 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 89: setting nstcomm equal to nstcalcenergy for less overhead 89: 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: Generating 1-4 interactions: fudge = 0.5 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/tip3p5.gro' 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 3 NOTEs 89: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 89: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 7 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.003 0.001 185.3 89: (ns/day) (hour/ns) 89: Performance: 1034.264 0.023 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 89: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 89: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (992 ms) 89: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (15491 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 13 tests from 1 test suite ran. (15497 ms total) 89: [ PASSED ] 13 tests. 89/96 Test #89: MdrunCoordinationConstraintsTests2Ranks ...... Passed 15.86 sec test 90 Start 90: MdrunFEPTests 90: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 14 tests from 2 test suites. 90: [----------] Global test environment set-up. 90: [----------] 2 tests from ExpandedEnsembleTest 90: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 79.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun '30 atom system in water' 90: 16 steps, 0.0 ps. 90: Generated 2485 of the 2485 non-bonded parameter combinations 90: 90: Generated 2485 of the 2485 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'nonanol' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.270 0.135 199.9 90: (ns/day) (hour/ns) 90: Performance: 10.874 2.207 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 90: 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun '30 atom system in water' 90: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 90: 90: Writing final coordinates. 90: 90: NOTE: 11 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.131 0.066 199.7 90: (ns/day) (hour/ns) 90: Performance: 11.827 2.029 90: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (259 ms) 90: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 79.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 2 NOTEs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun '30 atom system in water' 90: 1 steps, 0.0 ps. 90: Generated 2485 of the 2485 non-bonded parameter combinations 90: 90: Generated 2485 of the 2485 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'nonanol' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/nonanol_vacuo.gro' 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 16 % of the run time was spent in pair search, 90: you might want to increase nstlist (this has no effect on accuracy) 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.042 0.021 199.6 90: (ns/day) (hour/ns) 90: Performance: 8.284 2.897 90: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (37 ms) 90: [----------] 2 tests from ExpandedEnsembleTest (296 ms total) 90: 90: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 3 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -1613519706 90: 90: Generated 153 of the 153 non-bonded parameter combinations 90: 90: Generated 153 of the 153 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'ASN' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.94 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.882 0.441 200.0 90: (ns/day) (hour/ns) 90: Performance: 4.113 5.835 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 90: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10887 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 3 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -67175481 90: 90: Generated 153 of the 153 non-bonded parameter combinations 90: 90: Generated 153 of the 153 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'ASN' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.94 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.857 0.428 200.0 90: (ns/day) (hour/ns) 90: Performance: 4.235 5.667 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (521 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 90: With PME there is a minor soft core effect present at the cut-off, 90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 90: energy conservation, but usually other effects dominate. With a common 90: sigma value of 0.34 nm the fraction of the particle-particle potential at 90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 4 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -169883778 90: 90: Generated 153 of the 153 non-bonded parameter combinations 90: 90: Generated 153 of the 153 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'ASN' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.94 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.657 0.328 200.0 90: (ns/day) (hour/ns) 90: Performance: 5.525 4.344 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (422 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 90: With PME there is a minor soft core effect present at the cut-off, 90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 90: energy conservation, but usually other effects dominate. With a common 90: sigma value of 0.34 nm the fraction of the particle-particle potential at 90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: 90: NOTE 3 [file topol.top, line 155]: 90: System has non-zero total charge: 1.000000 90: Total charge should normally be an integer. See 90: https://manual.gromacs.org/current/user-guide/floating-point.html 90: for discussion on how close it should be to an integer. 90: 90: 90: 90: 90: WARNING 2 [file topol.top, line 155]: 90: You are using Ewald electrostatics in a system with net charge. This can 90: lead to severe artifacts, such as ions moving into regions with low 90: dielectric, due to the uniform background charge. We suggest to 90: neutralize your system with counter ions, possibly in combination with a 90: physiological salt concentration. 90: 90: Setting the LD random seed to -16393 90: 90: Generated 171 of the 171 non-bonded parameter combinations 90: 90: Generated 171 of the 171 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Excluding 1 bonded neighbours molecule type 'NA' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'ASN' 90: 90: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 90: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 90: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 90: Charge 90: J. Chem. Theory Comput. (2014) 90: DOI: 10.1021/ct400626b 90: -------- -------- --- Thank You --- -------- -------- 90: 90: Number of degrees of freedom in T-Coupling group System is 358.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 5 NOTEs 90: 90: There were 2 WARNINGs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: There are: 1 Ion residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 90: 90: Estimate for the relative computational load of the PME mesh part: 0.96 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 1.062 0.531 200.0 90: (ns/day) (hour/ns) 90: Performance: 3.416 7.026 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (22116 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 90: With PME there is a minor soft core effect present at the cut-off, 90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 90: energy conservation, but usually other effects dominate. With a common 90: sigma value of 0.34 nm the fraction of the particle-particle potential at 90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: 90: NOTE 3 [file topol.top, line 165]: 90: System has non-zero total charge: 1.000000 90: Total charge should normally be an integer. See 90: https://manual.gromacs.org/current/user-guide/floating-point.html 90: for discussion on how close it should be to an integer. 90: 90: 90: 90: 90: WARNING 2 [file topol.top, line 165]: 90: You are using Ewald electrostatics in a system with net charge. This can 90: lead to severe artifacts, such as ions moving into regions with low 90: dielectric, due to the uniform background charge. We suggest to 90: neutralize your system with counter ions, possibly in combination with a 90: physiological salt concentration. 90: 90: Setting the LD random seed to -557973537 90: 90: Generated 190 of the 190 non-bonded parameter combinations 90: 90: Generated 190 of the 190 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Excluding 1 bonded neighbours molecule type 'NA' 90: 90: turning H bonds into constraints... 90: 90: Excluding 1 bonded neighbours molecule type 'CL' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'CL' 90: 90: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 90: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 90: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 90: Charge 90: J. Chem. Theory Comput. (2014) 90: DOI: 10.1021/ct400626b 90: -------- -------- --- Thank You --- -------- -------- 90: 90: Number of degrees of freedom in T-Coupling group System is 361.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 5 NOTEs 90: 90: There were 2 WARNINGs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: There are: 2 Ion residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 90: 90: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 90: 90: Estimate for the relative computational load of the PME mesh part: 0.96 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 1.328 0.664 200.0 90: (ns/day) (hour/ns) 90: Performance: 2.732 8.784 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (757 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 90: For proper sampling of the (nearly) decoupled state, stochastic dynamics 90: should be used 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 90: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 90: and vdw_modifier=Force-switch 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 4 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 100 steps, 0.1 ps. 90: Setting the LD random seed to 2001293019 90: 90: Generated 153 of the 153 non-bonded parameter combinations 90: 90: Generated 153 of the 153 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Coupling 1 copies of molecule type 'ASN' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.94 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 4.792 2.396 200.0 90: (ns/day) (hour/ns) 90: Performance: 3.642 6.589 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (2569 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: 90: WARNING 2 [file topol.top, line 72]: 90: No default Bond types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '7 8 1'. 90: 90: 90: WARNING 3 [file topol.top, line 73]: 90: No default Bond types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '7 9 1'. 90: 90: 90: WARNING 4 [file topol.top, line 98]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '6 5 7 1'. 90: 90: 90: WARNING 5 [file topol.top, line 99]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '5 7 8 1'. 90: 90: 90: WARNING 6 [file topol.top, line 100]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '5 7 9 1'. 90: 90: 90: WARNING 7 [file topol.top, line 101]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '8 7 9 1'. 90: 90: 90: WARNING 8 [file topol.top, line 111]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '1 5 7 8 3'. 90: 90: 90: WARNING 9 [file topol.top, line 112]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '1 5 7 9 3'. 90: 90: 90: WARNING 10 [file topol.top, line 113]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '6 5 7 8 3'. 90: 90: 90: WARNING 11 [file topol.top, line 114]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '6 5 7 9 3'. 90: 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 2 NOTEs 90: 90: There were 11 WARNINGs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -2449409 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.95 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 1.085 0.542 200.0 90: (ns/day) (hour/ns) 90: Performance: 3.345 7.175 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (654 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: 90: WARNING 2 [file topol.top, line 72]: 90: No default Bond types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '7 8 1'. 90: 90: 90: WARNING 3 [file topol.top, line 73]: 90: No default Bond types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '7 9 1'. 90: 90: 90: WARNING 4 [file topol.top, line 98]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '6 5 7 1'. 90: 90: 90: WARNING 5 [file topol.top, line 99]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '5 7 8 1'. 90: 90: 90: WARNING 6 [file topol.top, line 100]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '5 7 9 1'. 90: 90: 90: WARNING 7 [file topol.top, line 101]: 90: No default Angle types for perturbed atoms in interaction, using normal 90: values. The interaction was 90: '8 7 9 1'. 90: 90: 90: WARNING 8 [file topol.top, line 111]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '1 5 7 8 3'. 90: 90: 90: WARNING 9 [file topol.top, line 112]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '1 5 7 9 3'. 90: 90: 90: WARNING 10 [file topol.top, line 113]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '6 5 7 8 3'. 90: 90: 90: WARNING 11 [file topol.top, line 114]: 90: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 90: normal values. The interaction was 90: '6 5 7 9 3'. 90: 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 90: Removing center of mass motion in the presence of position restraints 90: might cause artifacts. When you are using position restraints to 90: equilibrate a macro-molecule, the artifacts are usually negligible. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 3 NOTEs 90: 90: There were 11 WARNINGs 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to 1539211263 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.94 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 1.099 0.549 200.0 90: (ns/day) (hour/ns) 90: Performance: 3.302 7.268 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (643 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 2 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -391417669 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.89 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.522 0.261 200.0 90: (ns/day) (hour/ns) 90: Performance: 6.952 3.452 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (350 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: There was 1 NOTE 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.545 0.272 199.9 90: (ns/day) (hour/ns) 90: Performance: 6.661 3.603 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -1091050785 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.90 90: 90: This run will generate roughly 0 Mb of data 90: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (366 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 90: With PME there is a minor soft core effect present at the cut-off, 90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 90: energy conservation, but usually other effects dominate. With a common 90: sigma value of 0.34 nm the fraction of the particle-particle potential at 90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 3 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -636130481 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.95 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.867 0.434 200.0 90: (ns/day) (hour/ns) 90: Performance: 4.184 5.736 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (513 ms) 90: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 90: With PME there is a minor soft core effect present at the cut-off, 90: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 90: energy conservation, but usually other effects dominate. With a common 90: sigma value of 0.34 nm the fraction of the particle-particle potential at 90: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 90: 90: 90: WARNING 1 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 90: The Berendsen thermostat does not generate the correct kinetic energy 90: distribution, and should not be used for new production simulations (in 90: our opinion). We would recommend the V-rescale thermostat. 90: 90: Generating 1-4 interactions: fudge = 0.5 90: Number of degrees of freedom in T-Coupling group System is 355.00 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 90: For free energy simulations, the optimal load limit increases from 0.5 to 90: 0.667 90: 90: 90: 90: There were 3 NOTEs 90: 90: There was 1 WARNING 90: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 90: Changing nstlist from 10 to 100, rlist from 1 to 1 90: 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'AA' 90: 20 steps, 0.0 ps. 90: Setting the LD random seed to -1090605329 90: 90: Generated 136 of the 136 non-bonded parameter combinations 90: 90: Generated 136 of the 136 1-4 parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'ASN' 90: 90: turning H bonds into constraints... 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: turning H bonds into constraints... 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 90: Analysing residue names: 90: There are: 1 Protein residues 90: There are: 56 Water residues 90: Analysing Protein... 90: 90: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 0.90 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.578 0.289 200.0 90: (ns/day) (hour/ns) 90: Performance: 6.276 3.824 90: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (366 ms) 90: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (40173 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 14 tests from 2 test suites ran. (40478 ms total) 90: [ PASSED ] 14 tests. 90/96 Test #90: MdrunFEPTests ................................ Passed 40.59 sec test 91 Start 91: MdrunPullTests 91: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunPullTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 4 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 4 tests from PullTest/PullIntegrationTest 91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'r_1' has 3 atoms 91: Pull group 2 'r_2' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 1293.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 91: NVE simulation: will use the initial temperature of 303.122 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 0.575 nm 0.600 nm 91: 91: There was 1 NOTE 91: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI process 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 20 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.279 0.140 199.9 91: (ns/day) (hour/ns) 91: Performance: 12.992 1.847 91: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (511 ms) 91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'r_1' has 3 atoms 91: Pull group 2 'r_2' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 1293.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 91: NVE simulation: will use the initial temperature of 303.122 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 0.301 nm 0.400 nm 91: 91: There was 1 NOTE 91: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI process 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 20 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.203 0.102 199.9 91: (ns/day) (hour/ns) 91: Performance: 17.858 1.344 91: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (356 ms) 91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'r_1' has 3 atoms 91: Pull group 2 'r_2' has 3 atoms 91: Pull group 3 'r_3' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 1292.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 91: NVE simulation: will use the initial temperature of 303.357 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 0.575 nm 0.500 nm 91: 1 3 2 91: 3 3 8 0.331 nm 0.400 nm 91: 91: There was 1 NOTE 91: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI process 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 20 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.427 0.213 199.9 91: (ns/day) (hour/ns) 91: Performance: 8.499 2.824 91: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (671 ms) 91: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 91: Generating 1-4 interactions: fudge = 0.5 91: Pull group 1 'r_1' has 3 atoms 91: Pull group 2 'r_2' has 3 atoms 91: Number of degrees of freedom in T-Coupling group System is 1293.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 91: NVE simulation: will use the initial temperature of 303.122 K for 91: determining the Verlet buffer size 91: 91: Pull group natoms pbc atom distance at start reference at t=0 91: 1 3 2 91: 2 3 5 0.575 nm 0.000 nm 91: 1 3 2 91: 2 3 5 0.050 nm 0.000 nm 91: 91: There was 1 NOTE 91: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 1 MPI process 91: Using 2 OpenMP threads 91: 91: 91: NOTE: The number of threads is not equal to the number of (logical) cpus 91: and the -pin option is set to auto: will not pin threads to cpus. 91: This can lead to significant performance degradation. 91: Consider using -pin on (and -pinoffset in case you run multiple jobs). 91: starting mdrun 'spc2' 91: 20 steps, 0.0 ps. 91: Generated 330891 of the 330891 non-bonded parameter combinations 91: 91: Generated 330891 of the 330891 1-4 parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/spc216.gro' 91: 91: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 91: 91: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: 91: This run will generate roughly 0 Mb of data 91: 91: Writing final coordinates. 91: 91: NOTE: 20 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.392 0.196 199.9 91: (ns/day) (hour/ns) 91: Performance: 9.253 2.594 91: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (830 ms) 91: [----------] 4 tests from PullTest/PullIntegrationTest (2370 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 4 tests from 1 test suite ran. (2374 ms total) 91: [ PASSED ] 4 tests. 91/96 Test #91: MdrunPullTests ............................... Passed 2.54 sec test 92 Start 92: MdrunRotationTests 92: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunRotationTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 12 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 12 tests from RotationWorks/RotationTest 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 92: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: trr version: GMX_trn_file (single precision) 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -778115074 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.447 0.223 199.9 92: (ns/day) (hour/ns) 92: Performance: 20.105 1.194 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (306 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 92: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -50594561 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 21 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.480 0.240 199.9 92: (ns/day) (hour/ns) 92: Performance: 18.715 1.282 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (279 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 92: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -67267074 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 16 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.461 0.231 200.0 92: (ns/day) (hour/ns) 92: Performance: 19.472 1.233 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (274 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 92: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -1073807553 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 21 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.336 0.168 199.9 92: (ns/day) (hour/ns) 92: Performance: 26.710 0.899 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (184 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 92: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -1679819778 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 22 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.405 0.203 200.0 92: (ns/day) (hour/ns) 92: Performance: 22.155 1.083 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (218 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 92: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -67158100 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 28 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.379 0.189 199.9 92: (ns/day) (hour/ns) 92: Performance: 23.728 1.011 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (201 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 92: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -557900065 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 22 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.380 0.190 199.9 92: (ns/day) (hour/ns) 92: Performance: 23.612 1.016 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (213 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 92: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -141238529 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 22 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.428 0.214 200.0 92: (ns/day) (hour/ns) 92: Performance: 20.994 1.143 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (226 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 92: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -286007561 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 15 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.386 0.193 200.0 92: (ns/day) (hour/ns) 92: Performance: 23.259 1.032 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (223 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 92: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -1168130305 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 14 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.461 0.231 199.9 92: (ns/day) (hour/ns) 92: Performance: 19.471 1.233 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (261 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 92: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -19007214 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 20 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.369 0.185 199.9 92: (ns/day) (hour/ns) 92: Performance: 24.317 0.987 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (212 ms) 92: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 92: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: Rotation group 0 'system' has 4 atoms 92: Number of degrees of freedom in T-Coupling group rest is 9.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: Enforced rotation: group 0 has 4 reference positions. 92: Reading them from /build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/rotref.0.trr. 92: 92: There were 2 NOTEs 92: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 1 MPI process 92: Using 2 OpenMP threads 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 92: 25 steps, 0.1 ps. 92: Setting the LD random seed to -830476296 92: 92: Generated 1 of the 1 non-bonded parameter combinations 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonA' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonB' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonC' 92: 92: Excluding 1 bonded neighbours molecule type 'ArgonD' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 92: 92: This run will generate roughly 0 Mb of data 92: 92: Writing final coordinates. 92: 92: NOTE: 30 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.334 0.167 199.9 92: (ns/day) (hour/ns) 92: Performance: 26.913 0.892 92: Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 92: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 92: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (174 ms) 92: [----------] 12 tests from RotationWorks/RotationTest (2797 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 12 tests from 1 test suite ran. (2801 ms total) 92: [ PASSED ] 12 tests. 92/96 Test #92: MdrunRotationTests ........................... Passed 3.01 sec test 93 Start 93: MdrunSimulatorComparison 93: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 93: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 93: Test timeout computed to be: 600 93: [==========] Running 0 tests from 0 test suites. 93: [==========] 0 tests from 0 test suites ran. (0 ms total) 93: [ PASSED ] 0 tests. 93: 93: YOU HAVE 82 DISABLED TESTS 93: 93/96 Test #93: MdrunSimulatorComparison ..................... Passed 0.12 sec test 94 Start 94: MdrunVirtualSiteTests 94: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.1/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.1/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 94: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests 94: Test timeout computed to be: 600 94: [==========] Running 37 tests from 2 test suites. 94: [----------] Global test environment set-up. 94: [----------] 1 test from VirtualSiteVelocityTest 94: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 94: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 94: [----------] 1 test from VirtualSiteVelocityTest (4 ms total) 94: 94: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 94: NVE simulation with an initial temperature of zero: will use a Verlet 94: buffer of 10%. Check your energy drift! 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 11.1%. 94: The balanceable part of the MD step is 38%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 4.2%. 94: 94: 94: NOTE: 39 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.003 0.002 194.4 94: (ns/day) (hour/ns) 94: Performance: 442.386 0.054 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: trr version: GMX_trn_file (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: trr version: GMX_trn_file (single precision) 94: 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (71 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 94: Reading virtual site types... 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 94: NVE simulation with an initial temperature of zero: will use a Verlet 94: buffer of 10%. Check your energy drift! 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 11.5%. 94: The balanceable part of the MD step is 36%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 4.1%. 94: 94: 94: NOTE: 28 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 188.5 94: (ns/day) (hour/ns) 94: Performance: 905.341 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (44 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 94: NVE simulation with an initial temperature of zero: will use a Verlet 94: buffer of 10%. Check your energy drift! 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: 94: This run will generate roughly 0 Mb of data 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 8.9%. 94: The balanceable part of the MD step is 1%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.1%. 94: 94: 94: NOTE: 96 % of the run time was spent in domain decomposition, 94: 0 % of the run time was spent in pair search, 94: you might want to increase nstlist (this has no effect on accuracy) 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.042 0.021 199.5 94: (ns/day) (hour/ns) 94: Performance: 36.958 0.649 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (48 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 32 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 188.9 94: (ns/day) (hour/ns) 94: Performance: 873.107 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (79 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 187.1 94: (ns/day) (hour/ns) 94: Performance: 914.864 0.026 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (81 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 94: Generated 3 of the 6 non-bonded parameter combinations 94: Reading virtual site types... 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.014 0.007 198.4 94: (ns/day) (hour/ns) 94: Performance: 111.921 0.214 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 94: 1 94: 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (91 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: Reading virtual site types... 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 5 NOTEs 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.2 94: (ns/day) (hour/ns) 94: Performance: 918.212 0.026 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 94: 1 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (80 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: Reading virtual site types... 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 5 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 187.5 94: (ns/day) (hour/ns) 94: Performance: 922.237 0.026 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (74 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 94: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 94: 1 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 5 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 5 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.001 0.001 187.5 94: (ns/day) (hour/ns) 94: Performance: 994.054 0.024 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (45 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 94: NVE simulation with an initial temperature of zero: will use a Verlet 94: buffer of 10%. Check your energy drift! 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 9.7%. 94: The balanceable part of the MD step is 38%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 3.7%. 94: 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.9 94: (ns/day) (hour/ns) 94: Performance: 842.001 0.029 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (33 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 94: NVE simulation with an initial temperature of zero: will use a Verlet 94: buffer of 10%. Check your energy drift! 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 8.9%. 94: The balanceable part of the MD step is 42%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 3.8%. 94: 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.3 94: (ns/day) (hour/ns) 94: Performance: 885.793 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (29 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.2 94: (ns/day) (hour/ns) 94: Performance: 950.179 0.025 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (159 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 31 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 188.3 94: (ns/day) (hour/ns) 94: Performance: 876.627 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (75 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.3 94: (ns/day) (hour/ns) 94: Performance: 885.072 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (52 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 188.2 94: (ns/day) (hour/ns) 94: Performance: 793.936 0.030 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (57 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 190.4 94: (ns/day) (hour/ns) 94: Performance: 920.155 0.026 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (63 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Reading virtual site types... 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 30 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 188.7 94: (ns/day) (hour/ns) 94: Performance: 938.559 0.026 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (66 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2025.1/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.001 0.001 183.0 94: (ns/day) (hour/ns) 94: Performance: 959.544 0.025 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (47 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 32 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.002 0.001 189.0 94: (ns/day) (hour/ns) 94: Performance: 902.335 0.027 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (62 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: 94: 94: NOTE: 14 % of the run time was spent in domain decomposition, 94: 0 % of the run time was spent in pair search, 94: you might want to increase nstlist (this has no effect on accuracy) 94: 94: NOTE: 21 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.352 0.188 187.3 94: (ns/day) (hour/ns) 94: Performance: 4.137 5.801 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading virtual site types... 94: 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (552 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 94: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 94: that with the Verlet scheme, nstlist has no effect on the accuracy of 94: your simulation. 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: Generated 3 of the 6 non-bonded parameter combinations 94: 94: Excluding 3 bonded neighbours molecule type 'VSTEST' 94: 94: Cleaning up constraints and constant bonded interactions with virtual sites 94: Number of degrees of freedom in T-Coupling group System is 45.00 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 94: There are 6 non-linear virtual site constructions. Their contribution to 94: the energy error is approximated. In most cases this does not affect the 94: error significantly. 94: 94: 94: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 94: You are using a plain Coulomb cut-off, which might produce artifacts. 94: You might want to consider using PME electrostatics. 94: 94: 94: 94: This run will generate roughly 0 Mb of data 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 94: 94: Update groups can not be used for this system because an incompatible virtual site type is used 94: 94: Using 2 MPI processes 94: Using 1 OpenMP thread per MPI process 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Virtual sites test system in vacuo' 94: 8 steps, 0.0 ps. 94: 94: Writing final coordinates. 94: 94: NOTE: 29 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.001 0.001 188.9 94: (ns/day) (hour/ns) 94: Performance: 981.490 0.024 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: Reading file /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.1-Debian_2025.1_1 (single precision) 94: 94: Reading virtual site types... 94: Reading virtual site types... 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (78 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 94: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 94: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 94: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1986 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 37 tests from 2 test suites ran. (2059 ms total) 94: [ PASSED ] 37 tests. 94/96 Test #94: MdrunVirtualSiteTests ........................ Passed 2.33 sec test 95 Start 95: EnsembleHistogramPotentialPlugin.ForceCalc 95: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" 95: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests 95: Test timeout computed to be: 1500 95: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 95: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc 95: [==========] Running 1 test from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 1 test from EnsembleHistogramPotentialPlugin 95: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc 95: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) 95: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 1 test from 1 test suite ran. (0 ms total) 95: [ PASSED ] 1 test. 95/96 Test #95: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.11 sec test 96 Start 96: EnsembleBoundingPotentialPlugin.ForceCalc 96: Test command: /build/reproducible-path/gromacs-2025.1/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" 96: Working Directory: /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/tests 96: Test timeout computed to be: 1500 96: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 96: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc 96: [==========] Running 1 test from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 1 test from EnsembleBoundingPotentialPlugin 96: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc 96: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) 96: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 1 test from 1 test suite ran. (0 ms total) 96: [ PASSED ] 1 test. 96/96 Test #96: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.12 sec 100% tests passed, 0 tests failed out of 96 Label Time Summary: GTest = 1086.67 sec*proc (92 tests) IntegrationTest = 1006.37 sec*proc (31 tests) MpiTest = 798.99 sec*proc (23 tests) QuickGpuTest = 127.02 sec*proc (23 tests) SlowGpuTest = 921.01 sec*proc (14 tests) SlowTest = 66.69 sec*proc (14 tests) UnitTest = 13.62 sec*proc (47 tests) Total Test time (real) = 413.88 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.1/build/documentation/lib cmake /build/reproducible-path/gromacs-2025.1 \ -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMXAPI=ON \ -DGMX_PYTHON_PACKAGE=ON -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON -DGMX_BUILD_HELP=ON \ -DGMX_VERSION_STRING_OF_FORK="Debian-2025.1-1") -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.1/build/documentation/bin/gmx from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (55.0s) -- Generating done (3.2s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.1/build/documentation /usr/bin/make -j12 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles 67 /usr/bin/make -f CMakeFiles/Makefile2 docs/manual/CMakeFiles/manual.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make 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/build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/parser.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make 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Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.1/docs/reference-manual/analysis/plots/rdfO-O.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdfO-O.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.1/docs/reference-manual/analysis/plots/rdf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdf.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/eigensolver.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoption.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractsection.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-I/build/reproducible-path/gromacs-2025.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis/energyterm.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.28 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2025.1/admin -D GMX_CLANG_MINIMUM_REQUIRED_VERSION=14 -D GMX_GCC_MINIMUM_REQUIRED_VERSION=11 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2025.1 -D GMX_CUDA_MINIMUM_REQUIRED_COMPUTE_CAPABILITY=5.0 -D GMX_CUDA_MINIMUM_REQUIRED_VERSION=12.1 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2025.1/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Brian Andrews, Vladimir Basov, Paul Bauer, Hugh Bird, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Petter Johansson, Carsten Kutzner, Grzegorz Łazarski, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Lukas Müllender, Julien Nabet, Szilárd Páll, Andrea Pasquadibisceglie, Michele Pellegrino, Nicola Piasentin, Daniele Rapetti, Muhammad Umair Sadiq, Hubert Santuz, Roland Schulz, Michael Shirts, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermühle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Cathrine Bergh, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/index.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/texindex.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/download.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/links.dat /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/external/zlib/zutil.c cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/contribute.rst [ 2%] Built target tng_io_zlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.1/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/gitlab-ci.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/gitlab-ci.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-image-conversion-timestamp.txt cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/index.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst [ 8%] Built target sphinx-image-conversion /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs 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/build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/plots/mdpar.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/plots/mdpar.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/plots/parsort.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/plots/parsort.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/plots/ring.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/plots/ring.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/plots/shiftf.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/plots/shiftf.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/dd-cells.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/dd-cells.pdf [ 8%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.1/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -MF CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/muparser/src/muParserTokenReader.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/dd-tric.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/dd-tric.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/flowchart.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/flowchart.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/free1.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/free1.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/free2.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/free2.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/leapfrog.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/leapfrog.pdf [ 8%] Built target linearalgebra cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/lincs.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/lincs.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/maxwell.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/maxwell.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/mpmd-pme.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/mpmd-pme.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/algorithms/plots/nstric.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/nstric.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy 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-I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/dummies.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/dummies.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-bham.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-bham.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/fbposres.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fbposres.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-dih.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-dih.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-dr.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-dr.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/fig-02.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fig-02.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/fig-04.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/fig-04.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-imps.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-imps.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-lj.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-lj.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-morse.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-morse.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-pr.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-pr.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/f-rbs.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-rbs.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/ring-imp.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/ring-imp.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/softcore.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/softcore.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/gapsys-sc.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/gapsys-sc.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/subst-im.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/subst-im.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/tetra-im.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/tetra-im.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/vcrf.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vcrf.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/functions/plots/vsite-4fdn.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vsite-4fdn.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/awh-invN.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-invN.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/awh-pmfs.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-pmfs.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/awh-sampleweights.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-sampleweights.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/awh-traj.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-traj.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/compelsetup.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/compelsetup.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/dumaro.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/dumaro.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/dumtypes.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/dumtypes.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/equipotential.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/special/plots/equipotential.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/special/plots/field.pdf 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-I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsection.cpp cd 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/build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdfO-O.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/docs/reference-manual/analysis/plots/rdf.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdf.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionsvisitor.cpp [ 34%] Built target sphinx-input-rst cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/options && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/options/treesupport.cpp cd 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/build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_alb.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 35%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,--dependency-file=CMakeFiles/muparser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2025.1/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 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/build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. 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/build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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/build/reproducible-path/gromacs-2025.1/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/transformationcoordinate.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/modularsimulator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 38%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 43%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp: In member function 'std::pair gmx::TestParticleInsertion::performSingleInsertion(double, int64_t, bool, const gmx::RVec&, t_state*, gmx::MdrunScheduleWorkload*, gmx_wallcycle*, t_nrnb*)': /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:494:85: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 494 | t_nrnb* nrnb) | ^ cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.1/src/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.1/src -I/build/reproducible-path/gromacs-2025.1/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.1/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.1/src/external -isystem /build/reproducible-path/gromacs-2025.1/src/gromacs/../external/rpc_xdr -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.1/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.1/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.1/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.1/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.cpp cd 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/usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lm ../../lib/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.10.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.1/build/documentation/lib cd /build/reproducible-path/gromacs-2025.1/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi 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LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 586 undefined on input line 64613. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 586 undefined on input line 64638. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 586 undefined on input line 64638. [586] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 587 undefined on input line 64710. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 587 undefined on input line 64710. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 587 undefined on input line 64710. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 587 undefined on input line 64710. [587] Chapter 7. [588] [589] [590] [591] Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool [592] [593] [594] Chapter 8. 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[419 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.27 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45705 <./vsite-4fdn.pdf>] [420] [421] [422] [423 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46084 \end{equation} ] [424 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46169 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46169 \paragraph{Using LJ\sphinxhyphen{}PME} ] [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Underfull \vbox (badness 2368) detected at line 47444 [436] [437] [438] [439] [440] [441] Underfull \hbox (badness 10000) in paragraph at lines 48142--48145 []\T1/pcr/m/n/10 resA atomA nbondsA resB atomB nbondsB length newresA newresB [ atomI atomJ Overfull \hbox (10.25368pt too wide) in paragraph at lines 48349--48351 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 48362--48364 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 48378--48380 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48394--48396 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48403--48407 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48403--48407 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ [442] Underfull \hbox (badness 10000) in paragraph at lines 48444--48446 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 48457--48461 \T1/ptm/m/n/10 num-ber; residue [443] Underfull \hbox (badness 10000) in paragraph at lines 48595--48597 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 48598--48601 []|\T1/phv/m/n/10 num. 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[546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59226 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61338. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61338. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61525. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61525. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61724--61727 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62169. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62169. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62334. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62334. 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[596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 67999--68005 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69123--69129 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. 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Underfull \hbox (badness 10000) in paragraph at lines 73438--73442 \T1/ptm/m/n/10 (page 669[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73805--73809 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. 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Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31823. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 31823. [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Chapter 4. [321] [322] [323] [324] [325] [326] [327] [328] [329] Chapter 5. 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[495] [496] [497 <./field.pdf>] [498 <./compelsetup.pdf>] [499] [500] [501] [502 <./dumtypes.pdf> <./dumaro.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dumaro.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525 <./rdf.pdf>] [526 <./rdfO-O.pdf>] [527] [528] [529] [530 <./msdwater.pdf>] [531 <./dih-def.pdf> <./sgangle.pdf pdfTeX warning: /usr/bin/pdflatex (file ./sgangle.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [532 <./distm.pdf>] [533] [534] [535 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [536 <./phipsi.pdf>] [537 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [538] [539] [540 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58739 ...ecular shift (mol\sphinxhyphen{}shift)} ] [541] [542] [543 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 1}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59033 \end{equation} ] [544] [545 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59188 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59188 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59191 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59191 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59191 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59191 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... [546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59226 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61338. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61338. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61525. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61525. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61724--61727 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62169. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62169. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62334. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62334. 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[589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65279--65279 []\T1/ptm/m/n/10 Bool [593] [594] [595] Chapter 8. [596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 67999--68005 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69123--69129 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [626] [627] [628 <./redmine-states.png>] [629] [630] [631] [632] [633] [634] [635] Overfull \vbox (2.30272pt too high) detected at line 70272 [636] [637] [638] Overfull \vbox (1.24654pt too high) detected at line 70475 [639] Underfull \vbox (badness 10000) detected at line 70475 Underfull \vbox (badness 10000) detected at line 70475 [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71764. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71764. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71764. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71764. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71768. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71768. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71768. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71768. [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Chapter 9. [667] Chapter 10. Underfull \hbox (badness 10000) in paragraph at lines 73438--73442 \T1/ptm/m/n/10 (page 670[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73805--73809 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. [672] [673] Underfull \hbox (badness 10000) in paragraph at lines 74013--74021 [][][]\T1/ptm/m/n/10 Is-sue 5292[][] Cor-rectly sug-gest NEON over SVE for CPU builds on Neoverse-v2 at run Underfull \hbox (badness 10000) in paragraph at lines 74013--74021 \T1/ptm/m/n/10 time No longer sug-gest SVE over NEON for CPU builds on Neoverse -v2 at run time [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] Underfull \hbox (badness 7168) in paragraph at lines 75300--75305 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [687] [688] Underfull \hbox (badness 10000) in paragraph at lines 75458--75462 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 7722) in paragraph at lines 76771--76776 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Overfull \hbox (18.01631pt too wide) in paragraph at lines 87925--87928 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 87925--87928 [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] No file gromacs.ind. (./gromacs.aux) LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (839 pages, 13754687 bytes). 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/build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 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'/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 14%] Built target muparser [ 14%] Built target linearalgebra [ 16%] Built target options /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 17%] Built target gmx_objlib [ 19%] Built target energyanalysis [ 41%] Built target sphinx-input-rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 41%] Built target mdrun_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 41%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 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/build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 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'/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs 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/build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2025.1/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.1/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.1/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -j12 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage 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src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 8%] Built target lmfit_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/energyanalysis 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src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 16%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs 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-E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend [ 41%] Built target sphinx-input-rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen 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'/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2025.1/cmake/gmxConfigureVersionInfo.cmake /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build [ 41%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 41%] Built target doxygen-source-timestamp cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version [ 41%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 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make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 15 of file 'Doxyfile-xml' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 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'/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs /build/reproducible-path/gromacs-2025.1/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: 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/usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/manual /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.1/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/pdf.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 98%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/manual /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.1/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 98%] Built target manual /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2025.1/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.1/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.1/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule.cpp:64: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' at line 212 of file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 223 of file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule.cpp:168: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' at line 271 of file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 278 of file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' at line 286 of file /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:257: warning: @copydetails or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copybrief or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copydetails or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copybrief or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copydetails or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:278: warning: @copydetails or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 98%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2025.1/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2025.1 -B /build/reproducible-path/gromacs-2025.1/build/documentation -o /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/depgraphs /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... /build/reproducible-path/gromacs-2025.1/docs/doxygen/doxygenxml.py:35: SyntaxWarning: invalid escape sequence '\l' """Doxygen XML output parser. /build/reproducible-path/gromacs-2025.1/docs/doxygen/doxygenxml.py:343: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2025.1/docs/doxygen/doxygenxml.py:350: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" Scanning source tree... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [ 98%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/depgraphs NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/testasserts.h:738: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.1/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:57: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/iframeconverter.h:109: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:48: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:76: warning: Member CheckpointDataOperation (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:334: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.1/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (57), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (58), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (95), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.h:228: warning: unable to resolve reference to 'gmx_pme_reinit' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include/gromacs/timing/gpu_timing.h:57: warning: Member PmeStage (enumeration) of file gpu_timing.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:334: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:70: warning: Member SimulationRunnerMdpSource (enumeration) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:71: warning: Member awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:113: warning: Member awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int shareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:170: warning: Member awhParamSerialized(AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int biasShareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:62: warning: Member plumedKernelAvailable() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.cpp:402: warning: Member getNumberOfTestOpenMPThreads() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp:417: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target doxygen-lib /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ [ref.any] /build/reproducible-path/gromacs-2025.1/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run [ref.any] make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target webpage-sphinx The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'functions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'md_enums.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basicoptions.h' not generated, too many nodes (52), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'idef.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. warning: Included by graph for 'ifunc.h' not generated, too many nodes (91), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (371), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (252), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'enumerationhelpers.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (270), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (321), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (324), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes (230), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxy_gromacs_version.h:42: warning: Member COLVARPROXY_VERSION (macro definition) of file colvarproxy_gromacs_version.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:55: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:57: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:58: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:60: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:61: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:62: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:63: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:64: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:45: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:47: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:48: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:50: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:51: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:52: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:53: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:54: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/computemultibodycutoffs.cpp:278: warning: Member dd_bonded_cg_distance(const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb) (function) of file computemultibodycutoffs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:144: warning: Member dd_sendrecv2_rvec(const struct gmx_domdec_t gmx_unused *dd, int gmx_unused ddimind, rvec gmx_unused *buf_s_fw, int gmx_unused n_s_fw, rvec gmx_unused *buf_r_fw, int gmx_unused n_r_fw, rvec gmx_unused *buf_s_bw, int gmx_unused n_s_bw, rvec gmx_unused *buf_r_bw, int gmx_unused n_r_bw) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:230: warning: Member dd_bcast(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:240: warning: Member dd_scatter(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:259: warning: Member dd_gather(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:278: warning: Member dd_scatterv(const gmx_domdec_t gmx_unused *dd, gmx::ArrayRef< const int > gmx_unused scounts, gmx::ArrayRef< const int > gmx_unused disps, const T *sbuf, int rcount, T *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:321: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const int *sbuf, int rcount, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:328: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const gmx::RVec *sbuf, int rcount, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:336: warning: Member dd_gatherv(const gmx_domdec_t gmx_unused &dd, gmx::ArrayRef< const T > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > gmx_unused disps, gmx::ArrayRef< T > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:383: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const int > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< int > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_network.cpp:389: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const gmx::RVec > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< gmx::RVec > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:70: warning: Member supportedLibMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:73: warning: Member supportedThreadMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/localtopology.cpp:959: warning: Member dd_make_local_top(const gmx_domdec_t &dd, const gmx::DomdecZones &zones, int npbcdim, matrix box, rvec cellsize_min, const ivec npulse, t_forcerec *fr, ArrayRef< const RVec > coordinates, const gmx_mtop_t &mtop, gmx::ArrayRef< const int32_t > atomInfo, gmx_localtop_t *ltop) (function) of file localtopology.cpp is not documented. warning: Include graph for 'partition.cpp' not generated, too many nodes (61), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/reversetopology.cpp:412: warning: Member dd_make_reverse_top(FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking) (function) of file reversetopology.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/ewald.cpp:73: warning: Member cvec (typedef) of file ewald.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.cpp:578: warning: Member initGrids(gmx::ArrayRef< PmeAndFftGrids > gridsSet, const gmx_pme_t &pme, const bool requestReproducibility, gmx::ArrayRef< std::vector< AlignedVector< real > > > gridsStorage) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme.cpp:1799: warning: Member parallel_3dfft_destroy(gmx_parallel_3dfft *pfft_setup) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu_impl.h:58: warning: Member hardware_destructive_interference_size (variable) of file pme_force_sender_gpu_impl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gather_sycl.cpp:702: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gather_sycl.cpp:706: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu.cpp:280: warning: Member pme_gpu_launch_gather(gmx_pme_t *pme, gmx_wallcycle gmx_unused *wcycle, const real lambdaQ, const bool computeVirial) (function) of file pme_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:90: warning: Member mode (typedef) of file pme_gpu_calculate_splines_sycl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid.h:102: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid.h:107: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid.h:112: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid.h:116: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:61: warning: Member mode (typedef) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1404: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1409: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1414: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1418: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_hip_stubs.cpp:107: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *, bool) (function) of file pme_gpu_hip_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_internal.cpp:1127: warning: Member pme_gpu_update_input_box(PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_internal.cpp:2549: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_internal.h:70: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_internal.h:447: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:80: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:85: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:90: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:94: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:91: warning: Member INSTANTIATE_SPREAD_2( order, computeSplines, spreadCharges, numGrids, writeGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:94: warning: Member INSTANTIATE_SPREAD(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:100: warning: Member INSTANTIATE_GATHER_2(order, numGrids, readGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:103: warning: Member INSTANTIATE_GATHER(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:107: warning: Member INSTANTIATE_X(x, order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:113: warning: Member INSTANTIATE_SOLVE(subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:123: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:59: warning: Member c_pmeOrder (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:61: warning: Member c_wrapX (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:62: warning: Member c_wrapY (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:64: warning: Member c_stateA (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:65: warning: Member c_stateB (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp.cpp:484: warning: Member gmx_pme_send_resetcounters(const t_commrec gmx_unused *cr, int64_t gmx_unused step) (function) of file pme_pp.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:86: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:88: warning: Member PP_PME_RECVFTOGPU (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:90: warning: Member PP_PME_MDGPUGRAPH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_solve_sycl.cpp:54: warning: Member mode (typedef) of file pme_solve_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_spread_sycl.cpp:438: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_spread_sycl.cpp:444: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. warning: Included by graph for 'devicebuffer_datatype.h' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:73: warning: Member GMX_ALWAYS_INLINE (macro definition) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:100: warning: Member __attribute__((always_inline)) float gmxGpuFDim(const float one (function) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:100: warning: Member two (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:106: warning: Member value (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:124: warning: Member valueTwo (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:124: warning: Member valueThree (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:142: warning: Member d1 (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:142: warning: Member t (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpu_kernel_utils.h:147: warning: Member offset (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc.cpp:82: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc.cpp:87: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc_hip.cpp:91: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc_hip.cpp:95: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc_sycl.cpp:128: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *deviceContext) (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/pmalloc_sycl.cpp:137: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_hip.cpp:128: warning: Member determineIfDeviceHasLargeRegisterPool(std::string deviceArch) (function) of file device_management_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:68: warning: Member parseHardwareVersionNvidia(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:105: warning: Member getHardwareVersionNvidia(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:140: warning: Member parseHardwareVersionAmd(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:180: warning: Member getHardwareVersionAmd(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:214: warning: Member getHardwareVersionIntel(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:250: warning: Member getDeviceGpuAwareMpiStatus(const sycl::backend backend) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl.cpp:548: warning: Member partitionDevices(const std::vector< sycl::device > &&devices) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:51: warning: Member IntelProductConfig (enumeration) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:611: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:622: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:138: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:113: warning: Member staggeredAtomicAddForce(sycl::global_ptr< Float3 > gm_f, Float3 f, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:134: warning: Member harmonic_gpu(const float kA, const float xA, const float x, sycl::private_ptr< float > V, sycl::private_ptr< float > F) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:152: warning: Member bonds_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:260: warning: Member bond_angle_gpu(const sycl::float4 xi, const sycl::float4 xj, const sycl::float4 xk, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< float > costh, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:279: warning: Member angles_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:347: warning: Member urey_bradley_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:460: warning: Member dih_angle_gpu(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< int > t3) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:489: warning: Member dih_angle_gpu_sincos(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< float > cosval) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:529: warning: Member dopdihs_gpu(const float cpA, const float phiA, const int mult, const float phi, sycl::private_ptr< float > v, sycl::private_ptr< float > f) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:543: warning: Member do_dih_fup_gpu(const int i, const int j, const int k, const int l, const float ddphi, const Float3 r_ij, const Float3 r_kj, const Float3 r_kl, const Float3 m, const Float3 n, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const sycl::global_ptr< const Float4 > gm_xq, const int t1, const int t2, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:603: warning: Member pdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:649: warning: Member rbdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:761: warning: Member idihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:814: warning: Member pairs_gpu(const int i, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_iparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const float scale_factor, sycl::private_ptr< float > vtotVdw_loc, sycl::private_ptr< float > vtotElec_loc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/pairs.cpp:173: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:107: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:109: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:111: warning: Member pvEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:113: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:115: warning: Member virialEnergyFieldNames (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:119: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.cpp:132: warning: Member haveFepLambdaMoves(const t_inputrec &inputrec) (function) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constrtestrunners.h:63: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/leapfrogtestrunners.h:61: warning: Member GPU_LEAPFROG_SUPPORTED (macro definition) of file leapfrogtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/settletestrunners.h:61: warning: Member GPU_SETTLE_SUPPORTED (macro definition) of file settletestrunners.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:69: warning: Member sc_haveGpuConstraintSupport (variable) of file update_constrain_gpu_impl.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'mimic.cpp' not generated, too many nodes (64), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'minimize.cpp' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. warning: Include graph for 'rerun.cpp' not generated, too many nodes (66), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. warning: Include graph for 'runner.cpp' not generated, too many nodes (112), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. warning: Include graph for 'tpi.cpp' not generated, too many nodes (50), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp:186: warning: Member gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp:195: warning: Member gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp:204: warning: Member gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp:213: warning: Member gmx_sumli_sim(int gmx_unused nr, int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/multisim.cpp:391: warning: Member multisim_int_all_are_equal(const gmx_multisim_t *ms, int64_t value) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_simd.h:137: warning: Member GMX_HAVE_NBNXM_SIMD_4XM (macro definition) of file nbnxm_simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_gpu_buffer_ops_internal_sycl.cpp:50: warning: Member mode (typedef) of file nbnxm_gpu_buffer_ops_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:51: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_8 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:52: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_32 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:53: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_64 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_pruneonly.cpp:55: warning: Member mode (typedef) of file nbnxm_sycl_kernel_pruneonly.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/pbc.cpp:1433: warning: Member putAtomsInBoxTemplated(PbcType pbcType, const matrix box, const matrix boxDeformation, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v) (function) of file pbc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/pbc_simd.cpp:56: warning: Member set_pbc_simd(const t_pbc gmx_unused *pbc, real gmx_unused *pbc_simd) (function) of file pbc_simd.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:2029: warning: found documented return type for analyze_static that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:1844: warning: found documented return type for evaluate_boolean_static_part that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:1766: warning: found documented return type for init_method that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/compiler.cpp:1713: warning: found documented return type for process_const that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/params.cpp:905: warning: found documented return type for parse_values_enum that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_compare.cpp:364: warning: found documented return type for convert_real_int that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_compare.cpp:126: warning: found documented return type for init_compare that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_distance.cpp:102: warning: found documented return type for init_common that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_distance.cpp:120: warning: found documented return type for init_frame_common that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:255: warning: found documented return type for init_insolidangle that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_keywords.cpp:353: warning: found documented return type for init_kweval that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_keywords.cpp:113: warning: found documented return type for init_kwreal that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_keywords.cpp:365: warning: found documented return type for init_output_kweval that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_merge.cpp:77: warning: found documented return type for init_merge that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_permute.cpp:90: warning: found documented return type for init_permute that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp:100: warning: found documented return type for init_cog that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp:110: warning: found documented return type for init_com that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp:87: warning: found documented return type for init_kwpos that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_position.cpp:120: warning: found documented return type for init_output_pos that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_same.cpp:121: warning: found documented return type for init_same that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp:90: warning: found documented return type for check_molecules that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_simple.cpp:160: warning: found documented return type for check_pdbinfo that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:123: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:124: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:132: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:142: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:143: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:144: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:145: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/resourcedivision.cpp:149: warning: Member c_maxAutoTmpiRanksPerGpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include/gromacs/timing/instrumentation.h:216: warning: Member traceRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/include/gromacs/timing/instrumentation.h:217: warning: Member traceSubRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:198: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:130: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:143: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:156: warning: Member checkParticle(TestReferenceChecker *checker, const SimulationParticle &particle) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:201: warning: Member testParticleMassOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:202: warning: Member testParticleMassTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:203: warning: Member testParticleChargeOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:204: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:205: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/atoms.cpp:206: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/symtab.cpp:332: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (110), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxmpi.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. warning: Included by graph for 'logger.h' not generated, too many nodes (51), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. warning: Included by graph for 'gmxpre.h' not generated, too many nodes (792), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (98), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (113), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes (200), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testfilemanager.h' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selection.h:36: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_internal.h:115: warning: Member GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(bonded_threading_t) (function) of struct bonded_threading_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:121: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:122: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:137: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:138: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:139: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:140: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_pp_communication.h:141: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:106: warning: Member gmx_pme_pp(MPI_Comm simulationCommunicator, std::vector< PpRanks > &&ppRanks) (function) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:113: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:114: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:115: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:116: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:117: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_only.cpp:124: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:158: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:159: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:160: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:161: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:162: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:168: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:169: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:170: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/replicaexchange.cpp:171: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_types_host.h:263: warning: Member useNvshmem (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_types_host.h:265: warning: Member nvshmemParams (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:175: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl) (function) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:114: warning: Member splineKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member spreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member spreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member splineAndSpreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:119: warning: Member splineAndSpreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:120: warning: Member splineAndSpreadKernelWriteSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:121: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:122: warning: Member splineKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:123: warning: Member splineKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:124: warning: Member spreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:125: warning: Member spreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:126: warning: Member splineAndSpreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:127: warning: Member splineAndSpreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:128: warning: Member splineAndSpreadKernelWriteSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:142: warning: Member gatherKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:143: warning: Member gatherKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:144: warning: Member gatherKernelReadSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member gatherKernelReadSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member gatherKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member gatherKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member gatherKernelReadSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:149: warning: Member gatherKernelReadSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:159: warning: Member solveYZXKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:160: warning: Member solveXYZKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:161: warning: Member solveYZXEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:162: warning: Member solveXYZEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:163: warning: Member solveYZXKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:164: warning: Member solveXYZKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:165: warning: Member solveYZXEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:166: warning: Member solveXYZEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_program_impl.h:168: warning: Member nvshmemSignalKern (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/tables/forcetable.h:88: warning: Member t_forcetable(TableInteraction interaction, TableFormat format) (function) of struct t_forcetable is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnTpr (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnCoordSel (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:229: warning: Member bPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member min (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member max (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member dz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:243: warning: Member Temperature (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:259: warning: Member bBoundsOnly (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:270: warning: Member bTauIntGiven (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:281: warning: Member bHistEq (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:307: warning: Member bsMethod (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:310: warning: Member tauBootStrap (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:314: warning: Member histBootStrapBlockLength (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:320: warning: Member bs_verbose (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:326: warning: Member bTab (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabX (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabY (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabDz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxana/gmx_wham.cpp:328: warning: Member tabNbins (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/vsite_parm.cpp:99: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/vsite_parm.cpp:100: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/vsite_parm.cpp:101: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/vsite_parm.cpp:103: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/device_management_common.cpp:272: warning: Member operator()(const std::array< std::byte, N > &a) const noexcept (function) of struct anonymous_namespace{device_management_common.cpp}::HashAnArray is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/minimize.cpp:953: warning: Member mdModulesNotifiers (variable) of class anonymous_namespace{minimize.cpp}::EnergyEvaluator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:147: warning: Member AspartateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:169: warning: Member GlutamateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:191: warning: Member GlutamineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:213: warning: Member LysineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:234: warning: Member ArginineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1300: warning: Member ChainSeparationType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1562: warning: Member VSitesType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1573: warning: Member WaterType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1589: warning: Member MergeType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:127: warning: Member res2bb_notermini(const std::string &name, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:139: warning: Member enumValueToLongString(HistidineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:154: warning: Member enumValueToString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:161: warning: Member enumValueToLongString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:176: warning: Member enumValueToString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:183: warning: Member enumValueToLongString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:198: warning: Member enumValueToString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:205: warning: Member enumValueToLongString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:220: warning: Member enumValueToString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:226: warning: Member enumValueToLongString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:241: warning: Member enumValueToString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:248: warning: Member enumValueToLongString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:257: warning: Member select_res(int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:279: warning: Member get_asptp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:284: warning: Member get_glutp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:289: warning: Member get_glntp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:294: warning: Member get_lystp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:299: warning: Member get_argtp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:304: warning: Member get_histp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:309: warning: Member read_rtprename(const char *fname, FILE *fp, std::vector< RtpRename > *rtprename) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:367: warning: Member search_resrename(gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:413: warning: Member rename_resrtp(t_atoms *pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab *symtab, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:471: warning: Member pdbres_to_gmxrtp(t_atoms *pdba) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:484: warning: Member rename_pdbres(t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:579: warning: Member check_occupancy(t_atoms *atoms, const char *filename, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:642: warning: Member write_posres(const char *fn, t_atoms *pdba, real fc) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:671: warning: Member read_pdball(const char *inf, bool bOutput, const char *outf, char **title, t_atoms *atoms, rvec **x, PbcType *pbcType, matrix box, bool bRemoveH, t_symtab *symtab, const ResidueTypeMap &residueTypeMap, const char *watres, AtomProperties *aps, bool bVerbose) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:745: warning: Member process_chain(const gmx::MDLogger &logger, t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:835: warning: Member pdbicomp(const t_pdbindex &a, const t_pdbindex &b) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:853: warning: Member sort_pdbatoms(gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:939: warning: Member remove_duplicate_atoms(t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1011: warning: Member checkResidueTypeSanity(t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1085: warning: Member find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1320: warning: Member modify_chain_numbers(t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1444: warning: Member checkChainCyclicity(t_atoms *pdba, rvec *pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1309: warning: Member c_chainSeparationTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1312: warning: Member c_chainSeparationTypeNotificationMessages (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1569: warning: Member c_vsitesTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1585: warning: Member c_waterTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1596: warning: Member c_mergeTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state.cpp:95: warning: Member c_currentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/state.cpp:200: warning: Member c_dfHistoryCurrentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:73: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu_impl.h:74: warning: Member flag (variable) of struct gmx::CacheLineAlignedFlag is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:446: warning: Member mtop (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:447: warning: Member effectiveAtomDensity (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:448: warning: Member inputrec (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:449: warning: Member pressureTolerance (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:450: warning: Member listSetup (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:451: warning: Member useGpuList (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist_tuning.cpp:452: warning: Member mtsFactor (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/computeglobalselement.cpp:392: warning: Member getElementPointerImpl(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/computeglobalselement.cpp:426: warning: Member getElementPointerImpl(LegacySimulatorData *simulator, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/coordstate.h:86: warning: found documented return type for gmx::CoordState::sampleUmbrellaGridpoint that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_zones.h:104: warning: Member DomdecZones(ArrayRef< const int > ddDims) (function) of class gmx::DomdecZones is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:134: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:334: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:236: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/filenameoptionstorage.h:74: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::FileNameOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:162: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_zones.h:80: warning: Member x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_zones.h:82: warning: Member x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_zones.h:84: warning: Member bb_x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domdec_zones.h:86: warning: Member bb_x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:180: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:181: warning: Member pmeStream_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:105: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:106: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:107: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:108: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:109: warning: Member deviceStream_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:111: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:106: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:107: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:108: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:109: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:110: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:111: warning: Member context_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:112: warning: Member device_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:113: warning: Member commandQueue_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:115: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_rocfft.cpp:237: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:124: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:125: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:126: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:127: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:128: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:129: warning: Member queue_device_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:131: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/gpuforcereduction.h:125: warning: Member registerForcesReadyNvshmemFlags(DeviceBuffer< uint64_t > syncObj) (function) of class gmx::GpuForceReduction is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/gridset.h:137: warning: Member setNonLocalGrid(const int gridIndex, const int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::GridSet is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:115: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:95: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:133: warning: Member value (variable) of struct gmx::IsSerializableType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs.cpp:226: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs.cpp:227: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs.cpp:228: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs.cpp:229: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/lincs.cpp:230: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/mdgraph_gpu_impl.h:146: warning: Member Graph (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/mdgraph_gpu_impl.h:147: warning: Member GraphInstance (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:149: warning: Member kernel_noener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:150: warning: Member kernel_ener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:151: warning: Member kernel_noener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:152: warning: Member kernel_ener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:162: warning: Member kernel_memset_f (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:163: warning: Member kernel_memset_f2 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:164: warning: Member kernel_memset_f3 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.h:184: warning: Member nbnxn_atomdata_t(PinningPolicy pinningPolicy) (function) of struct gmx::nbnxn_atomdata_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/atomdata.h:224: warning: Member SimdMasks(NbnxmKernelType kernelType) (function) of struct gmx::nbnxn_atomdata_t::SimdMasks is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotforceprovider.h:65: warning: Member NNPotForceProvider(const NNPotParameters &, const MDLogger *logger) (function) of class gmx::NNPotForceProvider is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotoptions.h:108: warning: Member modelNeedsInput(const std::string &input) const (function) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/nnpotoptions.h:103: warning: Member numAtoms_ (variable) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/pme_force_sender_gpu_impl.h:138: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/qmmmforceprovider.h:69: warning: Member QMMMForceProvider(const QMMMParameters ¶meters, const LocalAtomSet &localQMAtomSet, const LocalAtomSet &localMMAtomSet, PbcType pbcType, const MDLogger &logger) (function) of class gmx::QMMMForceProvider is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/qmmm/qmmmtypes.h:142: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters) (function) of struct gmx::QMMMParameters is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/restraint/restraintmdmodule_impl.h:287: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:63: warning: Member ScalingMatrix(const Matrix3x3 &m) (function) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member xx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zz (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member yx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zy (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/evaluate.cpp:415: warning: found documented return type for gmx::SelectionEvaluator::evaluate that does not return anything /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinputhandle.h:139: warning: Member SimulationInputHandle(const SimulationInputHandle &source) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinputhandle.h:140: warning: Member SimulationInputHandle(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinputhandle.h:142: warning: Member operator=(const SimulationInputHandle &rhs) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulationinputhandle.h:143: warning: Member operator=(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/basicoptionstorage.h:191: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::StringOptionStorage is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdrun/tpi.cpp:177: warning: Member TestParticleInsertion(const t_inputrec &inputRec, const gmx_mtop_t &topGlobal, const gmx_localtop_t &top, const t_mdatoms &mdatoms, const MDModulesNotifiers &mdModulesNotifiers, t_forcerec *forceRec, gmx_enerdata_t *enerd, const Range< int > &testAtomsRange, ArrayRef< const RVec > xMoleculeToInsert, real beta, real rfExclusionEnergy, real referenceVolume, int numTasks, int taskIndex) (function) of class gmx::TestParticleInsertion is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/threaded_force_buffer.h:120: warning: Member processMask() (function) of class gmx::ThreadForceBuffer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:131: warning: Member update_coords(const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, t_state *state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata *fcdata, const gmx_ekindata_t *ekind, const Matrix3x3 &parrinelloRahmanM, int UpdatePart, const t_commrec *cr, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:147: warning: Member finish_update(const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, gmx::ArrayRef< const unsigned short > cFREEZE, t_state *state, gmx_wallcycle *wcycle, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:155: warning: Member update_sd_second_half(const t_inputrec &inputRecord, int64_t step, real *dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state *state, const t_commrec *cr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx::Constraints *constr, bool do_log, bool do_ene) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:169: warning: Member update_for_constraint_virial(const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:178: warning: Member update_temperature_constants(const t_inputrec &inputRecord, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:180: warning: Member getAndersenRandomizeGroup() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:182: warning: Member getBoltzmanFactor() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:184: warning: Member xp() (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/update.cpp:186: warning: Member deform() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/hbond.cpp:135: warning: Member HbondStorageFrame(int frnr, std::vector< HBond > data) (function) of struct gmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrame is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/msd.cpp:294: warning: Member MsdCoordinateManager(const int numAtoms, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeIndexMapping) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/msd.cpp:124: warning: Member MsdColumnProxy(std::vector< double > *column) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/msd.cpp:126: warning: Member push_back(double value) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/modules/msd.cpp:380: warning: Member MsdGroupData(const Selection &inputSel, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeAtomMapping) (function) of struct gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/domainpaircomm.cpp:242: warning: Member filterBondComm (variable) of struct gmx::anonymous_namespace{domainpaircomm.cpp}::DistanceCalculationInfo is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/freeenergydispatch.cpp:160: warning: Member dispatchFreeEnergyKernel(gmx::ArrayRef< const std::unique_ptr< t_nblist > > nbl_fep, const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, const bool clearForcesAndEnergies, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForceBuffer, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForeignEnergyBuffer, gmx_grppairener_t *foreignGroupPairEnergies, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb) (function) of namespace gmx::anonymous_namespace{freeenergydispatch.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:110: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t gmx_unused *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:112: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:120: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:122: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:136: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/simd_kernel.h:138: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:49: warning: Member c_nBoxZ (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:50: warning: Member c_nBoxY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:51: warning: Member c_nBoxX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:52: warning: Member c_numIvecs (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/options_impl.h:200: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl) (function) of class gmx::internal::OptionSectionImpl is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/awh_setup.h:74: warning: Member AwhTestParameters(ISerializer *serializer) (function) of struct gmx::test::AwhTestParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::GyrateInfo > is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::HbondInfo > is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/replicaexchange_equivalence.cpp:276: warning: Member operator()(const testing::TestParamInfo< ParamType > ¶meter) const (function) of struct gmx::test::PrintReplicaExchangeParametersToString is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:162: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:163: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:164: warning: Member mdpFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:165: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:166: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:167: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:168: warning: Member cptOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:169: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:170: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:171: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:172: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:173: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:174: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:175: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:176: warning: Member dhdlFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:177: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/moduletest.h:178: warning: Member maxwarn_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:73: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:74: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:75: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:86: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:87: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:104: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:106: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:112: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/toputils.h:113: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:147: warning: Member grid_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:148: warning: Member gridIndexToDataIndex_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:149: warning: Member data_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:150: warning: Member numColumns_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:151: warning: Member numRows_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/applied_forces/awh/tests/biasstate.cpp:152: warning: Member filename_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:361: warning: Member WriteFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:362: warning: Member TestFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:371: warning: Member addTestValues() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:389: warning: Member test() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:365: warning: Member writeFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:367: warning: Member testFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:437: warning: Member addTestValueFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:453: warning: Member testingTypes_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:467: warning: Member fileManager_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:468: warning: Member filename_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:77: warning: Member value (variable) of struct gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:184: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:190: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:196: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:202: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:208: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:118: warning: Member begin() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:119: warning: Member end() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:109: warning: Member Iterator(const T *ptr) (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:110: warning: Member operator++() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:111: warning: Member operator!=(const Iterator &other) const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/checkpointdata.cpp:112: warning: Member operator*() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/cmdlinetest.cpp:266: warning: Member ViewMatchesCString(const std::string_view view) (function) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/cmdlinetest.cpp:265: warning: Member view_ (variable) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:93: warning: Member currentState (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:94: warning: Member perLambdaInformation (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:95: warning: Member finalPos (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:82: warning: Member index (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member count (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member G (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member dG (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/tests/indexutil.cpp:102: warning: Member setGroup(const int(&atoms)[count]) (function) of class gmx::test::anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/nbnxm/tests/kernel_test.cpp:280: warning: Member KernelInputParameters(TupleT t) (function) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp:62: warning: Member setupMTop(gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds) (function) of namespace gmx::test::anonymous_namespace{massrepartitioning.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/hardware/tests/mockhardwaretopology.cpp:260: warning: Member runTest(const HardwareTopology &hwTop) (function) of class gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:361: warning: Member getNbList() (function) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:344: warning: Member idef (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:347: warning: Member chargeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:348: warning: Member chargeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:349: warning: Member typeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:350: warning: Member typeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:354: warning: Member iAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:355: warning: Member jAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:356: warning: Member shift (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:357: warning: Member gid (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:358: warning: Member exclFep (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/pairs.cpp:111: warning: Member OutputQuantities(int energyGroup) (function) of struct gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/parrinellorahman.cpp:149: warning: Member sc_boxShapeNames (variable) of namespace gmx::test::anonymous_namespace{parrinellorahman.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/parrinellorahman.cpp:180: warning: Member operator()(const Matrix3x3 &matrix) const (function) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/mdlib/tests/parrinellorahman.cpp:179: warning: Member prefix (variable) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.1/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::ScatteringInfo > is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/template_mp.cpp:49: warning: Member Options (enumeration) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/template_mp.cpp:58: warning: Member testEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/template_mp.cpp:64: warning: Member testBoolEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/utility/tests/template_mp.cpp:70: warning: Member testBoolDoubleOrNot(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests/timing.cpp:79: warning: Member delayInMilliseconds (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/timing/tests/timing.cpp:80: warning: Member wcycle (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.1/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. /build/reproducible-path/gromacs-2025.1/docs/doxygen/directories.cpp:96: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.1/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/docs /build/reproducible-path/gromacs-2025.1/build/documentation /build/reproducible-path/gromacs-2025.1/build/documentation/docs /build/reproducible-path/gromacs-2025.1/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/documentation' cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E remove -f /build/reproducible-path/gromacs-2025.1/build/documentation/docs/html/manual-2025.1-Debian_2025.1_1.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.1/build/documentation/docs/manual/gromacs.pdf /build/reproducible-path/gromacs-2025.1/build/documentation/docs/html/manual-2025.1-Debian_2025.1_1.pdf cd /build/reproducible-path/gromacs-2025.1/build/documentation/docs && /usr/bin/cmake -E echo "Webpage output: file:///build/reproducible-path/gromacs-2025.1/build/documentation/docs/html/index.html" Webpage output: file:///build/reproducible-path/gromacs-2025.1/build/documentation/docs/html/index.html make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/documentation' touch build-manual dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -j12 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2025.1/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 0%] Built target scanner [ 0%] Built target internal_rpc_xdr [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 2%] Built target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend [ 4%] Built target tng_io_obj /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 4%] Built target lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 4%] Built target linearalgebra make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 8%] Built target colvars_objlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 10%] Built target options [ 10%] Built target energyanalysis make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 10%] Built target mdrun_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 13%] Built target gmx_objlib [ 13%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 15%] Built target modularsimulator [ 15%] Built target taskassignment /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [ 97%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build [100%] Built target nblib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend [100%] Built target gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" [100%] Built target gmx /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build [100%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target _gmxapi make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build [100%] Built target gmxapi_extension_test make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' cd /build/reproducible-path/gromacs-2025.1/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.1/build/mpi /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.1/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' [100%] Built target gmxapi_extension make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/export.dlg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/defselection.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residues.xml -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: 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Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ss.map -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/random.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/phbres.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/atommass.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session/resources.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/context.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/status.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapi.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/traits.hpp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/setup.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/util.hpp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particlesequencer.h 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so.10 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_mpi.pc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs_mpi-config.cmake -- Installing: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-select.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-order.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-check.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi' /usr/bin/make -j12 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2025.1/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target scanner /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target thread_mpi [ 0%] Built target internal_rpc_xdr [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 0%] Built target tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 0%] Built target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build [ 0%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 0%] Built target energyanalysis make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 0%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory 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'/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib 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'/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.1/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory 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/build/reproducible-path/gromacs-2025.1/build/mpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util -- Up-to-date: 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-- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_mpi_d.pc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs-hints_mpi_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx_mpi_d -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1 -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/mpi-dp' /usr/bin/make -j12 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2025.1/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.1/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 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src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd 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/usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory 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'/build/reproducible-path/gromacs-2025.1/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [ 8%] Built target options [ 8%] Built target linearalgebra [ 12%] Built target colvars_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 12%] Built target gmx_objlib [ 12%] Built target energyanalysis make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' cd /build/reproducible-path/gromacs-2025.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic /build/reproducible-path/gromacs-2025.1/build/basic/src/gromacs/pulling 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for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/template/README -- 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/topology_enums.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/trajectory -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/fileio/trxio.h -- Installing: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdtypes -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/restraint -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/vector.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.10 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs/gromacs-hints.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic' /usr/bin/make -j12 -C build/basic-dp install DESTDIR=/build/reproducible-path/gromacs-2025.1/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.1 -B/build/reproducible-path/gromacs-2025.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 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make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.1-Debian_2025.1_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.1 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.1/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.1-1 -P /build/reproducible-path/gromacs-2025.1/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs 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make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 0%] Built target internal_rpc_xdr [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 6%] Built target tng_io_obj [ 6%] Built target scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend [ 6%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs /build/reproducible-path/gromacs-2025.1/build/basic-dp 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directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 6%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 6%] Built target linearalgebra make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 6%] Built target energyanalysis make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [ 10%] Built target colvars_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory 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'/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" [ 12%] Built target gmx_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.1/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make 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/build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib /build/reproducible-path/gromacs-2025.1/build/basic-dp 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gmxapi [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend [100%] Built target gmx make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' cd /build/reproducible-path/gromacs-2025.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.1 /build/reproducible-path/gromacs-2025.1/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.1/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.1/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/cmake/gromacs_d/gromacs-hints_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/share/man/man1/gmx-trajectory.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.1/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* perl -lne 'print' /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion.bash \ /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion-*.bash > \ /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/gmx-completion-concat mv /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/demux.pl /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/demux mv /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2025.1/debian/tmp/usr/bin/xplor2gmx dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_bash-completion -a dh_lintian -a dh_link -a dh_testdir -i dh_testroot -i dh_installdirs -i dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installman -i find /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc", found 24749 files. Now have 24749 files in total. Removed 0 files due to nonunique device and inode. Total size is 413940152 bytes or 395 MiB Removed 8194 files due to unique sizes from list. 16555 files left. Now eliminating candidates based on first bytes: removed 3528 files from list. 13027 files left. Now eliminating candidates based on last bytes: removed 1806 files from list. 11221 files left. Now eliminating candidates based on sha1 checksum: removed 3656 files from list. 7565 files left. It seems like you have 7565 files that are not unique Totally, 26 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 4404 links. symlinks -r -s -c /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/ absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2024/major/api.rst.txt changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> ../../2024/major/api.rst.txt absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> ../html-full/jquery.js absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> ../html-lib/dir_000021_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000089_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000088_000002.xhtml -> ../html-lib/dir_000089_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams.xhtml -> ../html-full/uniont__iparams.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000066_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000067_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000066_000002.xhtml -> ../html-lib/dir_000067_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000153_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000154_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000153_000002.xhtml -> ../html-lib/dir_000154_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000134_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000133_000002.xhtml -> ../html-lib/dir_000134_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> ../html-full/outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> ../html-full/doxygen.css absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/state_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> ../html-full/state_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/uniont__iparams-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/uniont__iparams-members.xhtml -> ../html-full/uniont__iparams-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> ../html-lib/dir_000009_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000019_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000019_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000019_000002.xhtml -> ../html-lib/dir_000019_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000073_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000072_000002.xhtml -> ../html-lib/dir_000073_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000086_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> ../html-lib/dir_000086_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hostallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> ../html-full/hostallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> ../html-lib/classgmx_1_1TextLineWrapper.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gammadistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> ../html-full/gammadistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputselector_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> ../html-full/outputselector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000152_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000151_000002.xhtml -> ../html-lib/dir_000152_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000074_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000075_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000074_000002.xhtml -> ../html-lib/dir_000075_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000007.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000023_000007.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000023_000007.xhtml -> ../html-lib/dir_000023_000007.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000091_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000092_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000091_000002.xhtml -> ../html-lib/dir_000092_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> ../html-full/classgmx_1_1NormalDistribution.xhtml absolute: 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-> ../html-lib/uniformrealdistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IAnalysisDataModule-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1IAnalysisDataModule-members.xhtml -> ../html-full/classgmx_1_1IAnalysisDataModule-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/selection_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h.xhtml -> 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../html-full/structgmx_1_1EnergyFunctionProperties-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml -> ../html-lib/dir_32e69e102eaf0237b7d1b4663f024c2e.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ListOfLists-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ListOfLists-members.xhtml -> ../html-full/classgmx_1_1ListOfLists-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000081_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000080_000002.xhtml -> ../html-lib/dir_000081_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__interaction__function.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__interaction__function.xhtml -> ../html-full/structt__interaction__function.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General-members.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataModuleSerial-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classForceHelperBuffers.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classForceHelperBuffers.xhtml -> ../html-full/classForceHelperBuffers.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/errorcodes_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/errorcodes_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/errorcodes_8h.xhtml -> ../html-lib/errorcodes_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000164_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000165_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000164_000002.xhtml -> ../html-lib/dir_000165_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError-members.xhtml -> ../html-full/classgmx_1_1MissingElementConnectionError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/threefry_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h.xhtml -> ../html-lib/threefry_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InconsistentInputError-members.xhtml -> ../html-full/classgmx_1_1InconsistentInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/outputselector_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h.xhtml -> ../html-lib/outputselector_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1InstallationPrefixInfo.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structgmx_1_1InstallationPrefixInfo.xhtml -> ../html-full/structgmx_1_1InstallationPrefixInfo.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ElementNotFoundError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ElementNotFoundError-members.xhtml -> ../html-full/classgmx_1_1ElementNotFoundError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ParallelConsistencyError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ParallelConsistencyError-members.xhtml -> ../html-full/classgmx_1_1ParallelConsistencyError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1InvalidInputError-members.xhtml -> ../html-full/classgmx_1_1InvalidInputError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CheckpointError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1CheckpointError-members.xhtml -> ../html-full/classgmx_1_1CheckpointError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution-members.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/pbcenums_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/pbcenums_8h.xhtml -> ../html-lib/pbcenums_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000112_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000113_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000112_000002.xhtml -> ../html-lib/dir_000113_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NotImplementedError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NotImplementedError-members.xhtml -> ../html-full/classgmx_1_1NotImplementedError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/register_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/register_8h.xhtml -> ../html-full/register_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tabulatednormaldistribution_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/tabulatednormaldistribution_8h.xhtml -> ../html-lib/tabulatednormaldistribution_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setatoms_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setatoms_8h.xhtml -> ../html-lib/setatoms_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml -> ../html-full/dir_991d69cdcf3b0071ea60d8f00677bf1a.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution-members.xhtml -> ../html-full/classgmx_1_1NormalDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution-members.xhtml -> ../html-full/classgmx_1_1GammaDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/setprecision_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/setprecision_8h.xhtml -> ../html-lib/setprecision_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SimulationInstabilityError-members.xhtml -> ../html-full/classgmx_1_1SimulationInstabilityError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/fixedcapacityvector_8h__incl.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/fixedcapacityvector_8h__incl.svg changed: 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/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000011_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000011_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000011_000002.xhtml -> ../html-lib/dir_000011_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000149_000002.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> ../html-lib/dir_000149_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3_dark.png -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_3_dark.png changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3_dark.png -> ../html-full/form_3_dark.png absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000092.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000093.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000159_000092.xhtml -> ../html-full/dir_000160_000093.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/form_3.png -> 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/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml -> ../html-full/src_2gromacs_2energyanalysis_2analysismodule_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000170.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000059_000170.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000059_000170.xhtml -> 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/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000162.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000160_000162.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000160_000162.xhtml -> ../html-full/dir_000160_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Double-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Double-members.xhtml -> ../html-full/classgmx_1_1Simd4Double-members.xhtml absolute: 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/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000162.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000021_000162.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000162.xhtml -> ../html-full/dir_000021_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000162.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000090_000162.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000090_000162.xhtml -> ../html-full/dir_000090_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDInt32-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDInt32-members.xhtml -> ../html-full/classgmx_1_1SimdDInt32-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFInt32-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFInt32-members.xhtml -> ../html-full/classgmx_1_1SimdFInt32-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrunutility.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__mdrunutility.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__mdrunutility.svg -> ../html-full/group__module__mdrunutility.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000162.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000066_000162.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000162.xhtml -> ../html-full/dir_000066_000162.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__nodecomm__t-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__nodecomm__t-members.xhtml -> ../html-full/structgmx__nodecomm__t-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDouble-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDouble-members.xhtml -> ../html-full/classgmx_1_1SimdDouble-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4Float-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4Float-members.xhtml -> ../html-full/classgmx_1_1Simd4Float-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4DBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4DBool-members.xhtml -> ../html-full/classgmx_1_1Simd4DBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Simd4FBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Simd4FBool-members.xhtml -> ../html-full/classgmx_1_1Simd4FBool-members.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdDIBool-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdDIBool-members.xhtml -> ../html-full/classgmx_1_1SimdDIBool-members.xhtml absolute: 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absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000158.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000065_000158.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000065_000158.xhtml -> ../html-full/dir_000065_000158.xhtml absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat-members.xhtml -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimdFloat-members.xhtml changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimdFloat-members.xhtml -> ../html-full/classgmx_1_1SimdFloat-members.xhtml absolute: 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absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enumvalues_13.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enumvalues_12.js -> ../../html-full/search/enumvalues_13.js absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_5.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_5.js -> ../../html-full/search/groups_5.js absolute: 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/build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_9.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> ../../html-full/search/related_9.js absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_d.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> ../../html-full/search/groups_d.js absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_b.js -> 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classgmx_1_1TorchModel__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.svg -> classgmx_1_1RestraintMDModule__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SwapCoordinates__inherit__graph.svg -> classgmx_1_1SwapCoordinates__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1QMMMOptions__inherit__graph.svg -> classgmx_1_1QMMMOptions__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.svg -> classgmx_1_1TextInputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NNPotForceProvider__inherit__graph.svg -> classgmx_1_1NNPotForceProvider__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.svg -> classgmx_1_1TextOutputFile__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ModularSimulator__inherit__graph.svg -> classgmx_1_1ModularSimulator__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_1e.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> all_1e.js absolute: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_2.js changed: /build/reproducible-path/gromacs-2025.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> all_2.js dh_bash-completion -i dh_lintian -i dh_link -i dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2025.1-1_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs10 -L libgromacs10 -l debian/libgromacs10/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -plibnblib-gmx0 -L libnblib-gmx0 -l debian/libnblib-gmx0/usr/lib:debian/libgromacs10/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -pgromacs -L libgromacs10 -l debian/libgromacs10/usr/lib:debian/gromacs/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libnblib-gmx-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs' in '../gromacs_2025.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs10' in '../libgromacs10_2025.1-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx-dev' in '../libnblib-gmx-dev_2025.1-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2025.1-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2025.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2025.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2025.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs10-dbgsym' in '../libgromacs10-dbgsym_2025.1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gromacs_2025.1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../gromacs_2025.1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3881455/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3881455 and its subdirectories I: Current time: Thu Mar 13 19:56:06 +14 2025 I: pbuilder-time-stamp: 1741845366